diff --git a/model/src/main/java/lcsb/mapviewer/model/graphics/ArrowType.java b/model/src/main/java/lcsb/mapviewer/model/graphics/ArrowType.java
index 8323caacba9439dff4ede31ec4d3e47e0b2e1480..d59fee3b9fcd39014094b3330a6b7fc011b89d57 100644
--- a/model/src/main/java/lcsb/mapviewer/model/graphics/ArrowType.java
+++ b/model/src/main/java/lcsb/mapviewer/model/graphics/ArrowType.java
@@ -26,7 +26,7 @@ public enum ArrowType {
* "data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAEEAAAAUCAYAAADStFABAAAAVElEQVR42u3WsQoAIAhFUf//p21qM0miQd890NISXKQyA4B+/HJPMoIrxQgjbCox0ghBDJeNMD1IOcIhSHpAy1XVfTK+TwJ3Aq8D/wR+jFPDAHizAFMtRsiqJUUMAAAAAElFTkSuQmCC"
* />
*/
- BLANK_CROSSBAR, //
+ BLANK_CROSSBAR,
/**
* The arrow end that should look as an image bellow. <br/>
@@ -36,7 +36,7 @@ public enum ArrowType {
* />
*
*/
- FULL_CROSSBAR, //
+ FULL_CROSSBAR,
/**
* The arrow end that should look as an image bellow. <br/>
@@ -46,7 +46,7 @@ public enum ArrowType {
* />
*
*/
- DIAMOND, //
+ DIAMOND,
/**
* The arrow end that should look as an image bellow. <br/>
@@ -55,7 +55,7 @@ public enum ArrowType {
* "data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAEEAAAAUCAYAAADStFABAAAATElEQVR42u3XMQ4AEBAFUfe/9ChEo5DVSPjzEgcwEVZrkvQHTDAikB6DKTkGq8TTwU5KEKoqMXh1nfrxZERv3jvB18E5wYnRv4N0RwevuDvTQl9v5wAAAABJRU5ErkJggg=="
* />
*/
- BLANK, //
+ BLANK,
/**
* The arrow end that should look as an image bellow. <br/>
@@ -65,7 +65,7 @@ public enum ArrowType {
* />
*
*/
- CROSSBAR, //
+ CROSSBAR,
/**
* The arrow end that should look as an image bellow. <br/>
@@ -74,7 +74,7 @@ public enum ArrowType {
* "data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAEEAAAAUCAYAAADStFABAAAASElEQVR42u3XgQkAIAzEwO6/9DtCVUQw5qALhIK2ShJMmuEH6NBDZBY1RFYRQ3wfIbtIIY5HyIvjJhjBCL4ORvDH6O3gFalLBns+vGCSjHRAAAAAAElFTkSuQmCC"
* /> *
*/
- CIRCLE, //
+ CIRCLE,
/**
* The arrow end that should look as an image bellow. <br/>
@@ -83,7 +83,7 @@ public enum ArrowType {
* "data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAEEAAAAUCAYAAADStFABAAAANklEQVR42u3UMQ4AQAQEQP//tGuUCrmSmcQDbJYIAFbJGoTRhyEQgXyeSx4cTfATLK7ulgeYehEYVKxEPu3IAAAAAElFTkSuQmCC"
* />
*/
- OPEN, //
+ OPEN,
/**
* The arrow end that should look as an image bellow. <br/>
@@ -92,7 +92,7 @@ public enum ArrowType {
* "data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAEEAAAAUCAYAAADStFABAAAAO0lEQVR42u3WsQ0AIAwDwey/tCloKF2TOykLvCLIDABfiQQ3wjsibI2RYkRoY2Th2ARvgt/BneBiBGgdPHh6hnF4gJ8AAAAASUVORK5CYII="
* />
*/
- FULL, //
+ FULL,
/**
* The arrow end that should look as an image bellow. <br/>
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java b/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
index 6502562e7c8f074b1b18ffcab2440956a8610c5c..292c6edb6bee84f68b93459ee5b08d1fe14077a4 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
@@ -23,386 +23,386 @@ import lcsb.mapviewer.model.map.species.Rna;
@SuppressWarnings("unchecked")
public enum MiriamType {
- BiGG_COMPARTMENT("BiGG Compartment", //
- "http://bigg.ucsd.edu/compartments/", //
- new String[] { "urn:miriam:bigg.compartment" }, //
- new Class<?>[] {}, "MIR:00000555"), //
+ BiGG_COMPARTMENT("BiGG Compartment",
+ "http://bigg.ucsd.edu/compartments/",
+ new String[] { "urn:miriam:bigg.compartment" },
+ new Class<?>[] {}, "MIR:00000555"),
- BiGG_METABOLITE("BiGG Metabolite", //
- "http://bigg.ucsd.edu/universal/metabolites", //
- new String[] { "urn:miriam:bigg.metabolite" }, //
- new Class<?>[] {}, "MIR:00000556"), //
+ BiGG_METABOLITE("BiGG Metabolite",
+ "http://bigg.ucsd.edu/universal/metabolites",
+ new String[] { "urn:miriam:bigg.metabolite" },
+ new Class<?>[] {}, "MIR:00000556"),
- BiGG_REACTIONS("BiGG Reaction", //
- "http://bigg.ucsd.edu/universal/reactions", //
- new String[] { "urn:miriam:bigg.reaction" }, //
- new Class<?>[] {}, "MIR:00000557"), //
+ BiGG_REACTIONS("BiGG Reaction",
+ "http://bigg.ucsd.edu/universal/reactions",
+ new String[] { "urn:miriam:bigg.reaction" },
+ new Class<?>[] {}, "MIR:00000557"),
/**
* Brenda enzyme database: http://www.brenda-enzymes.org.
*/
- BRENDA("BRENDA", //
- "http://www.brenda-enzymes.org", //
- new String[] { "urn:miriam:brenda" }, //
- new Class<?>[] {}, "MIR:00100101"), //
+ BRENDA("BRENDA",
+ "http://www.brenda-enzymes.org",
+ new String[] { "urn:miriam:brenda" },
+ new Class<?>[] {}, "MIR:00100101"),
/**
* Chemical Abstracts Service database: http://commonchemistry.org.
*/
- CAS("Chemical Abstracts Service", //
- "http://commonchemistry.org", //
- new String[] { "urn:miriam:cas" }, //
- new Class<?>[] {}, "MIR:00000237"), //
+ CAS("Chemical Abstracts Service",
+ "http://commonchemistry.org",
+ new String[] { "urn:miriam:cas" },
+ new Class<?>[] {}, "MIR:00000237"),
/**
* The Carbohydrate-Active Enzyme (CAZy) database: http://www.cazy.org/.
*/
- CAZY("CAZy", //
- "http://commonchemistry.org", //
- new String[] { "urn:miriam:cazy" }, //
- new Class<?>[] {}, "MIR:00000195"), //
+ CAZY("CAZy",
+ "http://commonchemistry.org",
+ new String[] { "urn:miriam:cazy" },
+ new Class<?>[] {}, "MIR:00000195"),
/**
* Consensus CDS: http://identifiers.org/ccds/.
*/
- CCDS("Consensus CDS", //
- "http://www.ncbi.nlm.nih.gov/CCDS/", //
- new String[] { "urn:miriam:ccds" }, //
- new Class<?>[] {}, "MIR:00000375"), //
+ CCDS("Consensus CDS",
+ "http://www.ncbi.nlm.nih.gov/CCDS/",
+ new String[] { "urn:miriam:ccds" },
+ new Class<?>[] {}, "MIR:00000375"),
/**
* Chebi database:
* <a href = "http://www.ebi.ac.uk/chebi/">http://www.ebi.ac.uk/chebi/</a>.
*/
- CHEBI("Chebi", //
- "http://www.ebi.ac.uk/chebi/", //
- new String[] { "urn:miriam:obo.chebi", "urn:miriam:chebi" }, //
- new Class<?>[] { Chemical.class, Drug.class, }, "MIR:00000002", //
- new Class<?>[] { Chemical.class }), //
+ CHEBI("Chebi",
+ "http://www.ebi.ac.uk/chebi/",
+ new String[] { "urn:miriam:obo.chebi", "urn:miriam:chebi" },
+ new Class<?>[] { Chemical.class, Drug.class, }, "MIR:00000002",
+ new Class<?>[] { Chemical.class }),
/**
* ChemSpider database:
* <a href = "http://www.chemspider.com/">http://www.chemspider.com/</a>.
*/
- CHEMSPIDER("ChemSpider", //
- "http://www.chemspider.com//", //
- new String[] { "urn:miriam:chemspider" }, //
- new Class<?>[] {}, "MIR:00000138"), //
+ CHEMSPIDER("ChemSpider",
+ "http://www.chemspider.com//",
+ new String[] { "urn:miriam:chemspider" },
+ new Class<?>[] {}, "MIR:00000138"),
/**
* Chembl database: https://www.ebi.ac.uk/chembldb/.
*/
- CHEMBL_COMPOUND("ChEMBL", //
- "https://www.ebi.ac.uk/chembldb/", //
- new String[] { "urn:miriam:chembl.compound" }, //
- new Class<?>[] { Drug.class }, "MIR:00000084"), //
+ CHEMBL_COMPOUND("ChEMBL",
+ "https://www.ebi.ac.uk/chembldb/",
+ new String[] { "urn:miriam:chembl.compound" },
+ new Class<?>[] { Drug.class }, "MIR:00000084"),
/**
* Target in chembl database: https://www.ebi.ac.uk/chembldb/.
*/
- CHEMBL_TARGET("ChEMBL target", //
- "https://www.ebi.ac.uk/chembldb/", //
- new String[] { "urn:miriam:chembl.target" }, //
- new Class<?>[] { Protein.class, Complex.class }, "MIR:00000085"), //
+ CHEMBL_TARGET("ChEMBL target",
+ "https://www.ebi.ac.uk/chembldb/",
+ new String[] { "urn:miriam:chembl.target" },
+ new Class<?>[] { Protein.class, Complex.class }, "MIR:00000085"),
/**
* Clusters of Orthologous Groups: https://www.ncbi.nlm.nih.gov/COG/.
*/
- COG("Clusters of Orthologous Groups", //
- "https://www.ncbi.nlm.nih.gov/COG/", //
- new String[] { "urn:miriam:cogs" }, //
- new Class<?>[] { Reaction.class }, "MIR:00000296"), //
+ COG("Clusters of Orthologous Groups",
+ "https://www.ncbi.nlm.nih.gov/COG/",
+ new String[] { "urn:miriam:cogs" },
+ new Class<?>[] { Reaction.class }, "MIR:00000296"),
/**
* Digital Object Identifier: http://www.doi.org/.
*/
- DOI("Digital Object Identifier", //
- "http://www.doi.org/", //
- new String[] { "urn:miriam:doi" }, //
- new Class<?>[] { Reaction.class }, "MIR:00000019"), //
+ DOI("Digital Object Identifier",
+ "http://www.doi.org/",
+ new String[] { "urn:miriam:doi" },
+ new Class<?>[] { Reaction.class }, "MIR:00000019"),
/**
* Drugbank database: http://www.drugbank.ca/.
*/
- DRUGBANK("DrugBank", //
- "http://www.drugbank.ca/", //
- new String[] { "urn:miriam:drugbank" }, //
- new Class<?>[] { Drug.class }, "MIR:00000102"), //
+ DRUGBANK("DrugBank",
+ "http://www.drugbank.ca/",
+ new String[] { "urn:miriam:drugbank" },
+ new Class<?>[] { Drug.class }, "MIR:00000102"),
/**
* Drugbank targets: http://www.drugbank.ca/targets.
*/
- DRUGBANK_TARGET_V4("DrugBank Target v4", //
- "http://www.drugbank.ca/targets", //
- new String[] { "urn:miriam:drugbankv4.target" }, //
- new Class<?>[] {}, "MIR:00000528"), //
+ DRUGBANK_TARGET_V4("DrugBank Target v4",
+ "http://www.drugbank.ca/targets",
+ new String[] { "urn:miriam:drugbankv4.target" },
+ new Class<?>[] {}, "MIR:00000528"),
/**
* Enzyme Nomenclature: http://www.enzyme-database.org/.
*/
- EC("Enzyme Nomenclature", //
- "http://www.enzyme-database.org/", //
- new String[] { "urn:miriam:ec-code" }, //
- new Class<?>[] { Protein.class, Complex.class }, "MIR:00000004"), //
+ EC("Enzyme Nomenclature",
+ "http://www.enzyme-database.org/",
+ new String[] { "urn:miriam:ec-code" },
+ new Class<?>[] { Protein.class, Complex.class }, "MIR:00000004"),
/**
* Ensembl: www.ensembl.org.
*/
- ENSEMBL("Ensembl", //
- "www.ensembl.org", //
- new String[] { "urn:miriam:ensembl" }, //
- new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000003"), //
+ ENSEMBL("Ensembl",
+ "www.ensembl.org",
+ new String[] { "urn:miriam:ensembl" },
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000003"),
/**
* Ensembl Plants: http://plants.ensembl.org/.
*/
- ENSEMBL_PLANTS("Ensembl Plants", //
- "http://plants.ensembl.org/", //
- new String[] { "urn:miriam:ensembl.plant" }, //
- new Class<?>[] {}, "MIR:00000205"), //
+ ENSEMBL_PLANTS("Ensembl Plants",
+ "http://plants.ensembl.org/",
+ new String[] { "urn:miriam:ensembl.plant" },
+ new Class<?>[] {}, "MIR:00000205"),
/**
* Entrez Gene: http://www.ncbi.nlm.nih.gov/gene.
*/
- ENTREZ("Entrez Gene", //
- "http://www.ncbi.nlm.nih.gov/gene", //
- new String[] { "urn:miriam:ncbigene", "urn:miriam:entrez.gene" }, //
- new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000069"), //
+ ENTREZ("Entrez Gene",
+ "http://www.ncbi.nlm.nih.gov/gene",
+ new String[] { "urn:miriam:ncbigene", "urn:miriam:entrez.gene" },
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000069"),
/**
* Gene Ontology: http://amigo.geneontology.org/amigo.
*/
- GO("Gene Ontology", //
- "http://amigo.geneontology.org/amigo", //
- new String[] { "urn:miriam:obo.go", "urn:miriam:go" }, //
- new Class<?>[] { Phenotype.class, Compartment.class, Complex.class }, "MIR:00000022"), //
+ GO("Gene Ontology",
+ "http://amigo.geneontology.org/amigo",
+ new String[] { "urn:miriam:obo.go", "urn:miriam:go" },
+ new Class<?>[] { Phenotype.class, Compartment.class, Complex.class }, "MIR:00000022"),
/**
* HGNC: http://www.genenames.org.
*/
- HGNC("HGNC", //
- "http://www.genenames.org", //
- new String[] { "urn:miriam:hgnc" }, //
- new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000080", //
- new Class<?>[] { Protein.class, Gene.class, Rna.class }), //
+ HGNC("HGNC",
+ "http://www.genenames.org",
+ new String[] { "urn:miriam:hgnc" },
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000080",
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }),
/**
* HGNC symbol: http://www.genenames.org.
*/
- HGNC_SYMBOL("HGNC Symbol", //
- "http://www.genenames.org", //
- new String[] { "urn:miriam:hgnc.symbol" }, //
- new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000362", //
- new Class<?>[] { Protein.class, Gene.class, Rna.class }), //
+ HGNC_SYMBOL("HGNC Symbol",
+ "http://www.genenames.org",
+ new String[] { "urn:miriam:hgnc.symbol" },
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000362",
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }),
/**
* HMDB: http://www.hmdb.ca/.
*/
- HMDB("HMDB", //
- "http://www.hmdb.ca/", //
- "urn:miriam:hmdb", //
- new Class<?>[] { Chemical.class, Drug.class, }, "MIR:00000051"), //
+ HMDB("HMDB",
+ "http://www.hmdb.ca/",
+ "urn:miriam:hmdb",
+ new Class<?>[] { Chemical.class, Drug.class, }, "MIR:00000051"),
/**
* InterPro: http://www.ebi.ac.uk/interpro/.
*/
- INTERPRO("InterPro", //
- "http://www.ebi.ac.uk/interpro/", //
- new String[] { "urn:miriam:interpro" }, //
- new Class<?>[] { Protein.class, Complex.class }, "MIR:00000011"), //
+ INTERPRO("InterPro",
+ "http://www.ebi.ac.uk/interpro/",
+ new String[] { "urn:miriam:interpro" },
+ new Class<?>[] { Protein.class, Complex.class }, "MIR:00000011"),
/**
* KEGG Compound: http://www.genome.jp/kegg/ligand.html.
*/
- KEGG_COMPOUND("Kegg Compound", //
- "http://www.genome.jp/kegg/ligand.html", //
- "urn:miriam:kegg.compound", //
- new Class<?>[] { Chemical.class }, "MIR:00000013"), //
+ KEGG_COMPOUND("Kegg Compound",
+ "http://www.genome.jp/kegg/ligand.html",
+ "urn:miriam:kegg.compound",
+ new Class<?>[] { Chemical.class }, "MIR:00000013"),
/**
* KEGG Genes: http://www.genome.jp/kegg/genes.html.
*/
- KEGG_GENES("Kegg Genes", //
- "http://www.genome.jp/kegg/genes.html", //
- new String[] { "urn:miriam:kegg.genes", "urn:miriam:kegg.genes:hsa" }, //
- new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000070"), //
+ KEGG_GENES("Kegg Genes",
+ "http://www.genome.jp/kegg/genes.html",
+ new String[] { "urn:miriam:kegg.genes", "urn:miriam:kegg.genes:hsa" },
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000070"),
/**
* KEGG Orthology: http://www.genome.jp/kegg/ko.html.
*/
- KEGG_ORTHOLOGY("KEGG Orthology", //
- "http://www.genome.jp/kegg/ko.html", //
- new String[] { "urn:miriam:kegg.orthology" }, //
- new Class<?>[] {}, "MIR:00000116"), //
+ KEGG_ORTHOLOGY("KEGG Orthology",
+ "http://www.genome.jp/kegg/ko.html",
+ new String[] { "urn:miriam:kegg.orthology" },
+ new Class<?>[] {}, "MIR:00000116"),
/**
* KEGG Pathway: http://www.genome.jp/kegg/pathway.html.
*/
- KEGG_PATHWAY("Kegg Pathway", //
- "http://www.genome.jp/kegg/pathway.html", //
- "urn:miriam:kegg.pathway", //
- new Class<?>[] { Reaction.class }, "MIR:00000012"), //
+ KEGG_PATHWAY("Kegg Pathway",
+ "http://www.genome.jp/kegg/pathway.html",
+ "urn:miriam:kegg.pathway",
+ new Class<?>[] { Reaction.class }, "MIR:00000012"),
/**
* KEGG Reaction: http://www.genome.jp/kegg/reaction/.
*/
- KEGG_REACTION("Kegg Reaction", //
- "http://www.genome.jp/kegg/reaction/", //
- "urn:miriam:kegg.reaction", //
- new Class<?>[] { Reaction.class }, "MIR:00000014"), //
+ KEGG_REACTION("Kegg Reaction",
+ "http://www.genome.jp/kegg/reaction/",
+ "urn:miriam:kegg.reaction",
+ new Class<?>[] { Reaction.class }, "MIR:00000014"),
/**
* MeSH 2012: http://www.nlm.nih.gov/mesh/.
*/
- MESH_2012("MeSH", //
- "http://www.nlm.nih.gov/mesh/", //
- new String[] { "urn:miriam:mesh" }, //
- new Class<?>[] { Phenotype.class, Compartment.class, Complex.class }, "MIR:00000270"), //
+ MESH_2012("MeSH",
+ "http://www.nlm.nih.gov/mesh/",
+ new String[] { "urn:miriam:mesh" },
+ new Class<?>[] { Phenotype.class, Compartment.class, Complex.class }, "MIR:00000270"),
/**
* miRBase Sequence: http://www.mirbase.org/.
*/
- MI_R_BASE_SEQUENCE("miRBase Sequence Database", //
- "http://www.mirbase.org/", //
- new String[] { "urn:miriam:mirbase" }, //
- new Class<?>[] {}, "MIR:00000078"), //
+ MI_R_BASE_SEQUENCE("miRBase Sequence Database",
+ "http://www.mirbase.org/",
+ new String[] { "urn:miriam:mirbase" },
+ new Class<?>[] {}, "MIR:00000078"),
/**
* miRBase Mature Sequence: http://www.mirbase.org/.
*/
- MI_R_BASE_MATURE_SEQUENCE("miRBase Mature Sequence Database", //
- "http://www.mirbase.org/", //
- new String[] { "urn:miriam:mirbase.mature" }, //
- new Class<?>[] {}, "MIR:00000235"), //
+ MI_R_BASE_MATURE_SEQUENCE("miRBase Mature Sequence Database",
+ "http://www.mirbase.org/",
+ new String[] { "urn:miriam:mirbase.mature" },
+ new Class<?>[] {}, "MIR:00000235"),
/**
* miRTaRBase Mature Sequence: http://mirtarbase.mbc.nctu.edu.tw/.
*/
- MIR_TAR_BASE_MATURE_SEQUENCE("miRTarBase Mature Sequence Database", //
- "http://mirtarbase.mbc.nctu.edu.tw/", //
- new String[] { "urn:miriam:mirtarbase" }, //
- new Class<?>[] {}, "MIR:00100739"), //
+ MIR_TAR_BASE_MATURE_SEQUENCE("miRTarBase Mature Sequence Database",
+ "http://mirtarbase.mbc.nctu.edu.tw/",
+ new String[] { "urn:miriam:mirtarbase" },
+ new Class<?>[] {}, "MIR:00100739"),
/**
* Mouse Genome Database: http://www.informatics.jax.org/.
*/
- MGD("Mouse Genome Database", //
- "http://www.informatics.jax.org/", //
- new String[] { "urn:miriam:mgd" }, //
- new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000037"), //
+ MGD("Mouse Genome Database",
+ "http://www.informatics.jax.org/",
+ new String[] { "urn:miriam:mgd" },
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000037"),
/**
* Online Mendelian Inheritance in Man: http://omim.org/.
*/
- OMIM("Online Mendelian Inheritance in Man", //
- "http://omim.org/", //
- new String[] { "urn:miriam:omim" }, //
- new Class<?>[] { Phenotype.class }, "MIR:00000016"), //
+ OMIM("Online Mendelian Inheritance in Man",
+ "http://omim.org/",
+ new String[] { "urn:miriam:omim" },
+ new Class<?>[] { Phenotype.class }, "MIR:00000016"),
/**
* PANTHER Family: http://www.pantherdb.org/.
*/
- PANTHER("PANTHER Family", //
- "http://www.pantherdb.org/", //
- new String[] { "urn:miriam:panther.family", "urn:miriam:panther" }, //
- new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000060"), //
+ PANTHER("PANTHER Family",
+ "http://www.pantherdb.org/",
+ new String[] { "urn:miriam:panther.family", "urn:miriam:panther" },
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000060"),
/**
* PDB: http://www.pdbe.org/.
*/
- PDB("Protein Data Bank", //
- "http://www.pdbe.org/", //
- "urn:miriam:pdb", //
+ PDB("Protein Data Bank",
+ "http://www.pdbe.org/",
+ "urn:miriam:pdb",
new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000020"),
/**
* Protein Family Database: http://pfam.xfam.org/.
*/
- PFAM("Protein Family Database", //
- "http://pfam.xfam.org//", //
- "urn:miriam:pfam", //
- new Class<?>[] {}, "MIR:00000028"), //
+ PFAM("Protein Family Database",
+ "http://pfam.xfam.org//",
+ "urn:miriam:pfam",
+ new Class<?>[] {}, "MIR:00000028"),
/**
* PharmGKB Pathways: http://www.pharmgkb.org/.
*/
- PHARM("PharmGKB Pathways", //
- "http://www.pharmgkb.org/", //
- "urn:miriam:pharmgkb.pathways", //
- new Class<?>[] {}, "MIR:00000089"), //
+ PHARM("PharmGKB Pathways",
+ "http://www.pharmgkb.org/",
+ "urn:miriam:pharmgkb.pathways",
+ new Class<?>[] {}, "MIR:00000089"),
/**
* PubChem-compound: http://pubchem.ncbi.nlm.nih.gov/.
*/
- PUBCHEM("PubChem-compound", //
- "http://pubchem.ncbi.nlm.nih.gov/", //
- new String[] { "urn:miriam:pubchem.compound" }, //
- new Class<?>[] { Chemical.class }, "MIR:00000034", //
- new Class<?>[] { Chemical.class }), //
+ PUBCHEM("PubChem-compound",
+ "http://pubchem.ncbi.nlm.nih.gov/",
+ new String[] { "urn:miriam:pubchem.compound" },
+ new Class<?>[] { Chemical.class }, "MIR:00000034",
+ new Class<?>[] { Chemical.class }),
/**
* PubChem-substance: http://pubchem.ncbi.nlm.nih.gov/.
*/
- PUBCHEM_SUBSTANCE("PubChem-substance", //
- "http://pubchem.ncbi.nlm.nih.gov/", //
- new String[] { "urn:miriam:pubchem.substance" }, //
- new Class<?>[] { Chemical.class }, "MIR:00000033", //
- new Class<?>[] { Chemical.class }), //
+ PUBCHEM_SUBSTANCE("PubChem-substance",
+ "http://pubchem.ncbi.nlm.nih.gov/",
+ new String[] { "urn:miriam:pubchem.substance" },
+ new Class<?>[] { Chemical.class }, "MIR:00000033",
+ new Class<?>[] { Chemical.class }),
/**
* PubMed: http://www.ncbi.nlm.nih.gov/PubMed/.
*/
- PUBMED("PubMed", //
- "http://www.ncbi.nlm.nih.gov/PubMed/", //
- new String[] { "urn:miriam:pubmed" }, //
- new Class<?>[] { BioEntity.class }, "MIR:00000015", //
- new Class<?>[] { Reaction.class }), //
+ PUBMED("PubMed",
+ "http://www.ncbi.nlm.nih.gov/PubMed/",
+ new String[] { "urn:miriam:pubmed" },
+ new Class<?>[] { BioEntity.class }, "MIR:00000015",
+ new Class<?>[] { Reaction.class }),
/**
* Reactome: http://www.reactome.org/.
*/
- REACTOME("Reactome", //
- "http://www.reactome.org/", //
- "urn:miriam:reactome", //
- new Class<?>[] { Reaction.class }, "MIR:00000018"), //
+ REACTOME("Reactome",
+ "http://www.reactome.org/",
+ "urn:miriam:reactome",
+ new Class<?>[] { Reaction.class }, "MIR:00000018"),
/**
* RefSeq: http://www.ncbi.nlm.nih.gov/projects/RefSeq/.
*/
- REFSEQ("RefSeq", //
- "http://www.ncbi.nlm.nih.gov/projects/RefSeq/", //
- "urn:miriam:refseq", //
+ REFSEQ("RefSeq",
+ "http://www.ncbi.nlm.nih.gov/projects/RefSeq/",
+ "urn:miriam:refseq",
new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000039"),
/**
* Rhea: http://www.rhea-db.org/.
*/
- RHEA("Rhea", //
- "http://www.rhea-db.org/", //
- "urn:miriam:rhea", //
+ RHEA("Rhea",
+ "http://www.rhea-db.org/",
+ "urn:miriam:rhea",
new Class<?>[] { Reaction.class }, "MIR:00000082"),
/**
* SGD: http://www.yeastgenome.org/.
*/
- SGD("Saccharomyces Genome Database", //
- "http://www.yeastgenome.org/", //
- "urn:miriam:sgd", //
+ SGD("Saccharomyces Genome Database",
+ "http://www.yeastgenome.org/",
+ "urn:miriam:sgd",
new Class<?>[] {}, "MIR:00000023"),
/**
* STITCH: http://stitch.embl.de/.
*/
- STITCH("STITCH", //
- "http://stitch.embl.de/", //
- "urn:miriam:stitch", //
+ STITCH("STITCH",
+ "http://stitch.embl.de/",
+ "urn:miriam:stitch",
new Class<?>[] {}, "MIR:00100343"),
/**
* STRING: http://string-db.org/.
*/
- STRING("STRING", //
- "http://string-db.org/", //
- "urn:miriam:string", //
+ STRING("STRING",
+ "http://string-db.org/",
+ "urn:miriam:string",
new Class<?>[] {}, "MIR:00000265"),
/**
@@ -411,105 +411,105 @@ public enum MiriamType {
* The name of a Locus is unique and used by TAIR, TIGR, and MIPS:
* http://arabidopsis.org/index.jsp.
*/
- TAIR_LOCUS("TAIR Locus", //
- "http://arabidopsis.org/index.jsp", //
- "urn:miriam:tair.locus", //
+ TAIR_LOCUS("TAIR Locus",
+ "http://arabidopsis.org/index.jsp",
+ "urn:miriam:tair.locus",
new Class<?>[] {}, "MIR:00000050"),
/**
* Taxonomy: http://www.ncbi.nlm.nih.gov/taxonomy/.
*/
- TAXONOMY("Taxonomy", //
- "http://www.ncbi.nlm.nih.gov/taxonomy/", //
- "urn:miriam:taxonomy", //
+ TAXONOMY("Taxonomy",
+ "http://www.ncbi.nlm.nih.gov/taxonomy/",
+ "urn:miriam:taxonomy",
new Class<?>[] {}, "MIR:00000006"),
/**
* Toxicogenomic: Chemical: http://ctdbase.org/detail.go.
* http://ctdbase.org/detail.go
*/
- TOXICOGENOMIC_CHEMICAL("Toxicogenomic Chemical", //
- "http://ctdbase.org/", //
- "urn:miriam:ctd.chemical", //
- new Class<?>[] {}, "MIR:00000098"), //
+ TOXICOGENOMIC_CHEMICAL("Toxicogenomic Chemical",
+ "http://ctdbase.org/",
+ "urn:miriam:ctd.chemical",
+ new Class<?>[] {}, "MIR:00000098"),
/**
* UniGene: http://www.ncbi.nlm.nih.gov/unigene.
*/
- UNIGENE("UniGene", //
- "http://www.ncbi.nlm.nih.gov/unigene", //
- "urn:miriam:unigene", //
+ UNIGENE("UniGene",
+ "http://www.ncbi.nlm.nih.gov/unigene",
+ "urn:miriam:unigene",
new Class<?>[] {}, "MIR:00000346"),
/**
* Uniprot: http://www.uniprot.org/.
*/
- UNIPROT("Uniprot", //
- "http://www.uniprot.org/", //
- "urn:miriam:uniprot", //
+ UNIPROT("Uniprot",
+ "http://www.uniprot.org/",
+ "urn:miriam:uniprot",
new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000005"),
/**
* UniProt Isoform: http://www.uniprot.org/.
*/
- UNIPROT_ISOFORM("UniProt Isoform", //
- "http://www.uniprot.org/", //
- "urn:miriam:uniprot.isoform", //
+ UNIPROT_ISOFORM("UniProt Isoform",
+ "http://www.uniprot.org/",
+ "urn:miriam:uniprot.isoform",
new Class<?>[] { Protein.class }, "MIR:00000388"),
/**
* Unknown reference type...
*/
- UNKNOWN("Unknown", //
- null, //
- new String[] {}, //
+ UNKNOWN("Unknown",
+ null,
+ new String[] {},
new Class<?>[] {}, null),
/**
* VMH metabolite: https://vmh.uni.lu/.
*/
- VMH_METABOLITE("VMH metabolite", //
- "https://vmh.uni.lu/", //
- new String[] { "urn:miriam:vmhmetabolite", "http://identifiers.org/vmhmetabolite/" }, //
+ VMH_METABOLITE("VMH metabolite",
+ "https://vmh.uni.lu/",
+ new String[] { "urn:miriam:vmhmetabolite", "http://identifiers.org/vmhmetabolite/" },
new Class<?>[] { Chemical.class }, "MIR:00000636"),
/**
* VMH reaction: https://vmh.uni.lu/.
*/
- VMH_REACTION("VMH reaction", //
- "https://vmh.uni.lu/", //
- new String[] { "urn:miriam:vmhreaction", "http://identifiers.org/vmhreaction/" }, //
+ VMH_REACTION("VMH reaction",
+ "https://vmh.uni.lu/",
+ new String[] { "urn:miriam:vmhreaction", "http://identifiers.org/vmhreaction/" },
new Class<?>[] { Reaction.class }, "MIR:00000640"),
/**
* Wikidata: https://www.wikidata.org/.
*/
- WIKIDATA("Wikidata", //
- "https://www.wikidata.org/", //
- new String[] { "urn:miriam:wikidata" }, //
- new Class<?>[] {}, "MIR:00000549"), //
+ WIKIDATA("Wikidata",
+ "https://www.wikidata.org/",
+ new String[] { "urn:miriam:wikidata" },
+ new Class<?>[] {}, "MIR:00000549"),
/**
* WikiPathways: http://www.wikipathways.org/.
*/
- WIKIPATHWAYS("WikiPathways", //
- "http://www.wikipathways.org/", //
- new String[] { "urn:miriam:wikipathways" }, //
- new Class<?>[] {}, "MIR:00000076"), //
+ WIKIPATHWAYS("WikiPathways",
+ "http://www.wikipathways.org/",
+ new String[] { "urn:miriam:wikipathways" },
+ new Class<?>[] {}, "MIR:00000076"),
/**
* Wikipedia: http://en.wikipedia.org/wiki/Main_Page.
*/
- WIKIPEDIA("Wikipedia (English)", //
+ WIKIPEDIA("Wikipedia (English)",
"http://en.wikipedia.org/wiki/Main_Page", // /
- new String[] { "urn:miriam:wikipedia.en" }, //
+ new String[] { "urn:miriam:wikipedia.en" },
new Class<?>[] {}, "MIR:00000384"),
/**
* WormBase: http://wormbase.bio2rdf.org/fct.
*/
- WORM_BASE("WormBase", //
+ WORM_BASE("WormBase",
"http://wormbase.bio2rdf.org/fct", // /
- new String[] { "urn:miriam:wormbase" }, //
+ new String[] { "urn:miriam:wormbase" },
new Class<?>[] {}, "MIR:00000027");
/**
diff --git a/model/src/main/java/lcsb/mapviewer/model/user/ConfigurationElementTypeGroup.java b/model/src/main/java/lcsb/mapviewer/model/user/ConfigurationElementTypeGroup.java
index 14bb318cbc8e65a4997d089a1dc1c6b8bbdc5683..55cc6ea9ed0f86b554ccfe656369552cdc4a614f 100644
--- a/model/src/main/java/lcsb/mapviewer/model/user/ConfigurationElementTypeGroup.java
+++ b/model/src/main/java/lcsb/mapviewer/model/user/ConfigurationElementTypeGroup.java
@@ -1,14 +1,14 @@
package lcsb.mapviewer.model.user;
public enum ConfigurationElementTypeGroup {
- EMAIL_NOTIFICATION("Email notification details"), //
- DEFAULT_USER_PRIVILEGES("Default user privileges"), //
- LEGEND_AND_LOGO("Legend and logo"), //
- OVERLAYS("Overlays"), //
- POINT_AND_CLICK("Point and click"), //
- SERVER_CONFIGURATION("Server configuration"), //
- LDAP_CONFIGURATION("LDAP configuration"), //
- SEARCH_VISIBLE_PARAMETERS("Search panel options"), //
+ EMAIL_NOTIFICATION("Email notification details"),
+ DEFAULT_USER_PRIVILEGES("Default user privileges"),
+ LEGEND_AND_LOGO("Legend and logo"),
+ OVERLAYS("Overlays"),
+ POINT_AND_CLICK("Point and click"),
+ SERVER_CONFIGURATION("Server configuration"),
+ LDAP_CONFIGURATION("LDAP configuration"),
+ SEARCH_VISIBLE_PARAMETERS("Search panel options"),
;
private String commonName;
diff --git a/model/src/test/java/lcsb/mapviewer/model/AllModelTests.java b/model/src/test/java/lcsb/mapviewer/model/AllModelTests.java
index f6e2540ef7f56a2d97febd6358f58971aa8a024b..c429322e36211a18135c790b3ddd682117a4c8d9 100644
--- a/model/src/test/java/lcsb/mapviewer/model/AllModelTests.java
+++ b/model/src/test/java/lcsb/mapviewer/model/AllModelTests.java
@@ -10,12 +10,12 @@ import lcsb.mapviewer.model.map.AllMapTests;
import lcsb.mapviewer.model.user.AllUserTests;
@RunWith(Suite.class)
-@SuiteClasses({ AllCacheTests.class, //
- AllGraphicsTests.class, //
- AllMapTests.class, //
- AllUserTests.class, //
- ProjectStatusTest.class, //
- ProjectTest.class,//
+@SuiteClasses({ AllCacheTests.class,
+ AllGraphicsTests.class,
+ AllMapTests.class,
+ AllUserTests.class,
+ ProjectStatusTest.class,
+ ProjectTest.class,
})
public class AllModelTests {
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/AllDbTests.java b/persist/src/test/java/lcsb/mapviewer/persist/AllDbTests.java
index 2c8aedbb1c088d42b23977d1cdb3ee30058d6efa..7b1483c9a2e71b555806eb256b4f405f9246f00e 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/AllDbTests.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/AllDbTests.java
@@ -7,11 +7,11 @@ import lcsb.mapviewer.persist.dao.AllDaoTests;
import lcsb.mapviewer.persist.mapper.AllMapperTests;
@RunWith(Suite.class)
-@Suite.SuiteClasses({ ApplicationContextLoaderTest.class, //
- AllDaoTests.class, //
- AllMapperTests.class, //
- DbUtilsTest.class, //
- SpringApplicationContextTest.class,//
+@Suite.SuiteClasses({ ApplicationContextLoaderTest.class,
+ AllDaoTests.class,
+ AllMapperTests.class,
+ DbUtilsTest.class,
+ SpringApplicationContextTest.class,
})
public class AllDbTests {
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/AllDaoTests.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/AllDaoTests.java
index 11c108067d9b0af5da41121c81f85c26a90cc44e..f3572bda9098e921e8110527bec20ff5a0599001 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/AllDaoTests.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/AllDaoTests.java
@@ -10,13 +10,13 @@ import lcsb.mapviewer.persist.dao.plugin.AllPluginTests;
import lcsb.mapviewer.persist.dao.user.AllUserTests;
@RunWith(Suite.class)
-@Suite.SuiteClasses({ AllCacheDbTests.class, //
- AllGraphicsDaoTests.class, //
- AllMapDaoTests.class, //
- AllPluginTests.class, //
- AllUserTests.class, //
- ConfigurationDaoTest.class, //
- ProjectDaoTest.class, //
+@Suite.SuiteClasses({ AllCacheDbTests.class,
+ AllGraphicsDaoTests.class,
+ AllMapDaoTests.class,
+ AllPluginTests.class,
+ AllUserTests.class,
+ ConfigurationDaoTest.class,
+ ProjectDaoTest.class,
})
public class AllDaoTests {
diff --git a/quadTrees/src/main/java/lcsb/mapviewer/utils/quadtree/quadtrees/PointQuadTree.java b/quadTrees/src/main/java/lcsb/mapviewer/utils/quadtree/quadtrees/PointQuadTree.java
index ac180b8682163ec851db397e8e32aa662eed02c2..a1d75c5ea6ca81228326bf8344b68be9105f721b 100644
--- a/quadTrees/src/main/java/lcsb/mapviewer/utils/quadtree/quadtrees/PointQuadTree.java
+++ b/quadTrees/src/main/java/lcsb/mapviewer/utils/quadtree/quadtrees/PointQuadTree.java
@@ -188,11 +188,11 @@ public class PointQuadTree {
* @return size of map within model.
*/
private MyRectangle getWholeField(IRectangleShape model) {
- // //////////////
+ // ////////////
int height, width = height = Math.max((int) (double) model.getHeight(), (int) (double) model.getWidth());
int x = 0;
int y = 0;
- // //////////////
+ // ////////////
Point tmp = new Point(x, y);
return new MyRectangle(tmp, width, height);
}
@@ -204,12 +204,12 @@ public class PointQuadTree {
* @return
*/
private MyRectangle getWholeField() {
- // //////////////
+ // ////////////
int height = DEFAULT_RECT_SIZE;
int width = DEFAULT_RECT_SIZE;
int x = 0;
int y = 0;
- // //////////////
+ // ////////////
Point tmp = new Point(x, y);
return new MyRectangle(tmp, width, height);
}
diff --git a/quadTrees/src/test/java/lcsb/mapviewer/utils/quadtree/SuitedTests.java b/quadTrees/src/test/java/lcsb/mapviewer/utils/quadtree/SuitedTests.java
index 7d6ec9b17997cd00310d24574d5ae8cfd8b2f535..b7fd39d7d93b839e1c3325b9608e98c1e1c7454f 100644
--- a/quadTrees/src/test/java/lcsb/mapviewer/utils/quadtree/SuitedTests.java
+++ b/quadTrees/src/test/java/lcsb/mapviewer/utils/quadtree/SuitedTests.java
@@ -12,12 +12,12 @@ import org.junit.runners.Suite;
public class SuitedTests {
}
-// ////////////////////////////////////////////////////
-//
+// //////////////////////////////////////////////////
+
// TODO TODO TODO TODO TODO TODO TODO TODO TODO
-//
+
// TESTOWAĆ TESTOWAĆ TESTOWAĆ TESTOWAĆ TESTOWAĆ
-//
+
// TODO TODO TODO TODO TODO TODO TODO TODO TODO
-//
-// ////////////////////////////////////////////////////
\ No newline at end of file
+
+// //////////////////////////////////////////////////
\ No newline at end of file
diff --git a/service/src/main/java/lcsb/mapviewer/services/utils/data/BuildInLayout.java b/service/src/main/java/lcsb/mapviewer/services/utils/data/BuildInLayout.java
index 8f30ecde5992625ca63ea397e685eeea258856b0..32dd39567fba98e4ccbe6e8675795ad765802df6 100644
--- a/service/src/main/java/lcsb/mapviewer/services/utils/data/BuildInLayout.java
+++ b/service/src/main/java/lcsb/mapviewer/services/utils/data/BuildInLayout.java
@@ -7,35 +7,35 @@ package lcsb.mapviewer.services.utils.data;
* @author Piotr Gawron
*
*/
-public enum BuildInLayout { //
+public enum BuildInLayout {
/**
* Normal strainghtforward visualization.
*/
- NORMAL("Network", "_normal", null, false), //
+ NORMAL("Network", "_normal", null, false),
// /**
// * Set of data containing Substantia Nigra data for Parkinson Disease (false
// * discovery ratio 0.01).
// */
// FDR_001("PD Substantia Nigra FDR=0.01", "_001", "/enricoData/ge001.txt",
- // false), //
+ // false),
// /**
// * Set of data containing Substantia Nigra data for Parkinson Disease (false
// * discovery ratio 0.05).
// */
// FDR_005("PD Substantia Nigra FDR=0.05", "_005", "/enricoData/ge005.txt",
- // false), //
+ // false),
// /**
// * Set of data containing aging data for Parkinson Disease .
// */
- // AGING("Aging", "_ageing", "/enricoData/ageing.txt", false), //
+ // AGING("Aging", "_ageing", "/enricoData/ageing.txt", false),
/**
* Standard visualization with hierarchical view.
*/
- NESTED("Pathways and compartments", "_nested", null, true), //
+ NESTED("Pathways and compartments", "_nested", null, true),
/**
* Clean visualization (with colors reset to black and white).
*/
- CLEAN("Empty", "_empty", null, false); //
+ CLEAN("Empty", "_empty", null, false);
/**
* Title of the layout.
diff --git a/service/src/main/java/lcsb/mapviewer/services/utils/data/ColorSchemaColumn.java b/service/src/main/java/lcsb/mapviewer/services/utils/data/ColorSchemaColumn.java
index 29fc6ada64de065ea85f97ef7884b6aaa1e1ec7c..6e593c9bf27b9f83744ae9f6599cbb392a71ad0b 100644
--- a/service/src/main/java/lcsb/mapviewer/services/utils/data/ColorSchemaColumn.java
+++ b/service/src/main/java/lcsb/mapviewer/services/utils/data/ColorSchemaColumn.java
@@ -18,113 +18,113 @@ public enum ColorSchemaColumn {
/**
* Name of the element.
*/
- NAME("name", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }), //
+ NAME("name", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }),
- GENE_NAME("gene_name", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }), //
+ GENE_NAME("gene_name", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }),
/**
* Name of the element.
*/
- MODEL_NAME("model_name", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }), //
+ MODEL_NAME("model_name", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }),
/**
* Value that will be transformed into new color.
*
* @see ColorSchemaColumn#COLOR
*/
- VALUE("value", new ColorSchemaType[] { ColorSchemaType.GENERIC }), //
+ VALUE("value", new ColorSchemaType[] { ColorSchemaType.GENERIC }),
/**
* In which compartment the element should be located.
*/
- COMPARTMENT("compartment", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }), //
+ COMPARTMENT("compartment", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }),
/**
* Class type of the element.
*/
- TYPE("type", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }), //
+ TYPE("type", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }),
/**
* New element/reaction color.
*/
- COLOR("color", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }), //
+ COLOR("color", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }),
/**
* Identifier of the element.
*/
- IDENTIFIER("identifier", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }), //
+ IDENTIFIER("identifier", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }),
/**
* Element identifier.
*/
- ELEMENT_IDENTIFIER("elementIdentifier", new ColorSchemaType[] { ColorSchemaType.GENERIC }), //
+ ELEMENT_IDENTIFIER("elementIdentifier", new ColorSchemaType[] { ColorSchemaType.GENERIC }),
/**
* Element identifier.
*/
@Deprecated
- REACTION_IDENTIFIER("reactionIdentifier", new ColorSchemaType[] { ColorSchemaType.GENERIC }), //
+ REACTION_IDENTIFIER("reactionIdentifier", new ColorSchemaType[] { ColorSchemaType.GENERIC }),
/**
* New line width of the reaction.
*/
- LINE_WIDTH("lineWidth", new ColorSchemaType[] { ColorSchemaType.GENERIC }), //
+ LINE_WIDTH("lineWidth", new ColorSchemaType[] { ColorSchemaType.GENERIC }),
/**
* Position where gene variants starts.
*/
- POSITION("position", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
+ POSITION("position", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }),
/**
* Original DNA of the variant.
*/
- ORIGINAL_DNA("original_dna", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
+ ORIGINAL_DNA("original_dna", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }),
/**
* Alternative DNA of the variant.
*/
- ALTERNATIVE_DNA("alternative_dna", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
+ ALTERNATIVE_DNA("alternative_dna", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }),
/**
* Short description of the entry.
*/
- DESCRIPTION("description", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT, ColorSchemaType.GENERIC }), //
+ DESCRIPTION("description", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT, ColorSchemaType.GENERIC }),
/**
* Variant references.
*/
- REFERENCES("references", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
+ REFERENCES("references", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }),
/**
* What's the {@link ReferenceGenomeType}.
*/
- REFERENCE_GENOME_TYPE("reference_genome_type", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
+ REFERENCE_GENOME_TYPE("reference_genome_type", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }),
/**
* {@link ReferenceGenome#version Version} of the reference genome.
*/
- REFERENCE_GENOME_VERSION("reference_genome_version", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
+ REFERENCE_GENOME_VERSION("reference_genome_version", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }),
/**
* Contig where variant was observed.
*/
- CONTIG("contig", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
+ CONTIG("contig", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }),
- CHROMOSOME("chromosome", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
+ CHROMOSOME("chromosome", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }),
- ALLEL_FREQUENCY("allele_frequency", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
+ ALLEL_FREQUENCY("allele_frequency", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }),
- VARIANT_IDENTIFIER("variant_identifier", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
+ VARIANT_IDENTIFIER("variant_identifier", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }),
/**
* Should the direction of reaction be reversed.
*/
- REVERSE_REACTION("reverseReaction", new ColorSchemaType[] { ColorSchemaType.GENERIC }), //
+ REVERSE_REACTION("reverseReaction", new ColorSchemaType[] { ColorSchemaType.GENERIC }),
/**
* Optional amino acid change in the variant.
*/
- AMINO_ACID_CHANGE("amino_acid_change", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }); //
+ AMINO_ACID_CHANGE("amino_acid_change", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT });
/**
* Default constructor that creates enum entry.
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest.java
index ad76543a9dc3a1a471d13399bf3f19babccd763a..5b5f03cfa5eff790c57143d6b0f173fe727ff008 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest.java
@@ -124,10 +124,10 @@ public class LayoutServiceTest extends ServiceTestFunctions {
assertTrue(layoutService.userCanAddLayout(model, user));
- CreateLayoutParams params = new CreateLayoutParams().name("Test").//
- directory("testDir").//
- model(model).//
- colorInputStream(new FileInputStream("testFiles/enricoData/ge001.txt")).//
+ CreateLayoutParams params = new CreateLayoutParams().name("Test").
+ directory("testDir").
+ model(model).
+ colorInputStream(new FileInputStream("testFiles/enricoData/ge001.txt")).
user(user);
Layout row = layoutService.createLayout(params);
@@ -159,10 +159,10 @@ public class LayoutServiceTest extends ServiceTestFunctions {
userService.setUserPrivilege(user, new Privilege(1, PrivilegeType.CUSTOM_LAYOUTS, user));
assertEquals(1, layoutService.getAvailableCustomLayoutsNumber(user));
- CreateLayoutParams params = new CreateLayoutParams().name("Test").//
- directory("testDir").//
- model(model).//
- colorInputStream(new FileInputStream("testFiles/enricoData/ge001.txt")).//
+ CreateLayoutParams params = new CreateLayoutParams().name("Test").
+ directory("testDir").
+ model(model).
+ colorInputStream(new FileInputStream("testFiles/enricoData/ge001.txt")).
user(user);
Layout row = layoutService.createLayout(params);
@@ -194,10 +194,10 @@ public class LayoutServiceTest extends ServiceTestFunctions {
userService.setUserPrivilege(user, new Privilege(1, PrivilegeType.CUSTOM_LAYOUTS, user));
- CreateLayoutParams params = new CreateLayoutParams().name("Test").//
- directory("testDir").//
- model(model).//
- colorInputStream(new FileInputStream("testFiles/enricoData/ge001.txt")).//
+ CreateLayoutParams params = new CreateLayoutParams().name("Test").
+ directory("testDir").
+ model(model).
+ colorInputStream(new FileInputStream("testFiles/enricoData/ge001.txt")).
user(user);
Layout row = layoutService.createLayout(params);
@@ -228,10 +228,10 @@ public class LayoutServiceTest extends ServiceTestFunctions {
userService.setUserPrivilege(user, new Privilege(1, PrivilegeType.CUSTOM_LAYOUTS, user));
- CreateLayoutParams params = new CreateLayoutParams().name("Test").//
- directory("testDir").//
- model(model).//
- colorInputStream(new FileInputStream("testFiles/enricoData/ge001.txt")).//
+ CreateLayoutParams params = new CreateLayoutParams().name("Test").
+ directory("testDir").
+ model(model).
+ colorInputStream(new FileInputStream("testFiles/enricoData/ge001.txt")).
user(user);
Layout row = layoutService.createLayout(params);
@@ -263,11 +263,11 @@ public class LayoutServiceTest extends ServiceTestFunctions {
assertEquals(0, layouts.size());
userService.setUserPrivilege(user, new Privilege(1, PrivilegeType.CUSTOM_LAYOUTS, user));
- CreateLayoutParams params = new CreateLayoutParams().name("Test").//
- directory("testDir").//
- model(model).//
- colorInputStream(new FileInputStream("testFiles/enricoData/ge001.txt")).//
- user(user).//
+ CreateLayoutParams params = new CreateLayoutParams().name("Test").
+ directory("testDir").
+ model(model).
+ colorInputStream(new FileInputStream("testFiles/enricoData/ge001.txt")).
+ user(user).
async(true);
long logCounter = getInfos().size();
@@ -326,10 +326,10 @@ public class LayoutServiceTest extends ServiceTestFunctions {
userService.setUserPrivilege(user, new Privilege(1, PrivilegeType.CUSTOM_LAYOUTS, user));
userService.setUserPrivilege(user, new ObjectPrivilege(localProject, 1, PrivilegeType.VIEW_PROJECT, user));
- CreateLayoutParams params = new CreateLayoutParams().name("Test").//
- directory("testDir").//
- model(localModel).//
- colorInputStream(new FileInputStream("testFiles/enricoData/ge001.txt")).//
+ CreateLayoutParams params = new CreateLayoutParams().name("Test").
+ directory("testDir").
+ model(localModel).
+ colorInputStream(new FileInputStream("testFiles/enricoData/ge001.txt")).
user(user);
layoutService.createLayout(params);
@@ -364,11 +364,11 @@ public class LayoutServiceTest extends ServiceTestFunctions {
assertEquals(0, layouts.size());
userService.setUserPrivilege(user, new Privilege(1, PrivilegeType.CUSTOM_LAYOUTS, user));
- CreateLayoutParams params = new CreateLayoutParams().name("Test").//
- directory("testDir").//
- model(model).//
- colorInputStream(new FileInputStream("testFiles/enricoData/ge001.txt")).//
- user(user).//
+ CreateLayoutParams params = new CreateLayoutParams().name("Test").
+ directory("testDir").
+ model(model).
+ colorInputStream(new FileInputStream("testFiles/enricoData/ge001.txt")).
+ user(user).
async(false);
Layout row = layoutService.createLayout(params);
@@ -400,11 +400,11 @@ public class LayoutServiceTest extends ServiceTestFunctions {
ByteArrayInputStream bais = new ByteArrayInputStream(
"name reactionIdentifier Color\ns1 #CC0000\ns2 #CCCC00\n re1 #CCCC00\n"
.getBytes(StandardCharsets.UTF_8));
- CreateLayoutParams params = new CreateLayoutParams().name("Test").//
- directory("testDir").//
- model(model).//
- colorInputStream(bais).//
- user(user).//
+ CreateLayoutParams params = new CreateLayoutParams().name("Test").
+ directory("testDir").
+ model(model).
+ colorInputStream(bais).
+ user(user).
async(false);
Layout row = layoutService.createLayout(params);
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java
index f2662d31704357f1359dfde340fdf11a30dc1aa5..7f87878305ca49d3c85f32690080fa9a9001ec5c 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java
@@ -132,16 +132,16 @@ public class ProjectServiceTest extends ServiceTestFunctions {
public void testUpdater() throws Exception {
try {
String project_id = "test_id";
- projectService.createProject(new CreateProjectParams().//
- authenticationToken(adminToken).//
- projectId(project_id).//
- version("").//
- projectFile("testFiles/centeredAnchorInModifier.xml").//
- annotations(true).//
- images(true).//
- async(false).//
- projectDir(tmpResultDir).//
- addUser("admin", "admin").//
+ projectService.createProject(new CreateProjectParams().
+ authenticationToken(adminToken).
+ projectId(project_id).
+ version("").
+ projectFile("testFiles/centeredAnchorInModifier.xml").
+ annotations(true).
+ images(true).
+ async(false).
+ projectDir(tmpResultDir).
+ addUser("admin", "admin").
analyzeAnnotations(true));
Project project = projectService.getProjectByProjectId(project_id, adminToken);
assertEquals(ProjectStatus.DONE, project.getStatus());
@@ -161,23 +161,23 @@ public class ProjectServiceTest extends ServiceTestFunctions {
ZipEntryFile entry3 = new ModelZipEntryFile("s2.xml", "s2", false, false, SubmodelType.UNKNOWN);
ZipEntryFile entry4 = new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN);
ZipEntryFile entry5 = new ModelZipEntryFile("mapping.xml", "mapping", false, true, SubmodelType.UNKNOWN);
- projectService.createProject(new CreateProjectParams().//
- authenticationToken(adminToken).//
- projectId(projectId).//
- version("").//
- complex(true).//
- projectFile("testFiles/complexModel/complex_model.zip").//
- addZipEntry(entry1).//
- addZipEntry(entry2).//
- addZipEntry(entry3).//
- addZipEntry(entry4).//
- addZipEntry(entry5).//
- annotations(true).//
- semanticZoomContainsMultipleLayouts(true).//
- images(true).//
- async(false).//
- projectDir(tmpResultDir).//
- addUser("admin", "admin").//
+ projectService.createProject(new CreateProjectParams().
+ authenticationToken(adminToken).
+ projectId(projectId).
+ version("").
+ complex(true).
+ projectFile("testFiles/complexModel/complex_model.zip").
+ addZipEntry(entry1).
+ addZipEntry(entry2).
+ addZipEntry(entry3).
+ addZipEntry(entry4).
+ addZipEntry(entry5).
+ annotations(true).
+ semanticZoomContainsMultipleLayouts(true).
+ images(true).
+ async(false).
+ projectDir(tmpResultDir).
+ addUser("admin", "admin").
analyzeAnnotations(true));
Project project = projectService.getProjectByProjectId(projectId, adminToken);
@@ -270,7 +270,7 @@ public class ProjectServiceTest extends ServiceTestFunctions {
model.addLayout(new Layout(BuildInLayout.NORMAL.getTitle(), path + "/normal", false));
model.addLayout(new Layout(BuildInLayout.NESTED.getTitle(), path + "/nested", false));
- CreateProjectParams params = new CreateProjectParams().images(true).//
+ CreateProjectParams params = new CreateProjectParams().images(true).
projectDir(tmpResultDir);
ProjectService pService = new ProjectService();
@@ -306,7 +306,7 @@ public class ProjectServiceTest extends ServiceTestFunctions {
model.addSubmodelConnection(new ModelSubmodelConnection(model2, SubmodelType.UNKNOWN, "name"));
- CreateProjectParams params = new CreateProjectParams().images(true).//
+ CreateProjectParams params = new CreateProjectParams().images(true).
projectDir(tmpResultDir);
ProjectService pService = new ProjectService();
@@ -337,20 +337,20 @@ public class ProjectServiceTest extends ServiceTestFunctions {
ZipEntryFile entry4 = new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN);
ZipEntryFile entry5 = new ModelZipEntryFile("mapping.xml", "mapping", false, true, SubmodelType.UNKNOWN);
- CreateProjectParams params = new CreateProjectParams().//
- projectId(projectId).//
- version("").//
- complex(true).//
- projectFile("testFiles/complexModel/complex_model_with_compartment.zip").//
- addZipEntry(entry1).//
- addZipEntry(entry2).//
- addZipEntry(entry3).//
- addZipEntry(entry4).//
- addZipEntry(entry5).//
- annotations(false).//
- images(false).//
- async(false).//
- projectDir(tmpResultDir).//
+ CreateProjectParams params = new CreateProjectParams().
+ projectId(projectId).
+ version("").
+ complex(true).
+ projectFile("testFiles/complexModel/complex_model_with_compartment.zip").
+ addZipEntry(entry1).
+ addZipEntry(entry2).
+ addZipEntry(entry3).
+ addZipEntry(entry4).
+ addZipEntry(entry5).
+ annotations(false).
+ images(false).
+ async(false).
+ projectDir(tmpResultDir).
analyzeAnnotations(false);
ComplexZipConverter parser = new ComplexZipConverter(CellDesignerXmlParser.class);
@@ -585,17 +585,17 @@ public class ProjectServiceTest extends ServiceTestFunctions {
}
zipFile.close();
- projectService.createProject(params.//
- authenticationToken(adminToken).//
- projectId(projectId).//
- version("").//
- complex(true).//
- projectFile(filename).//
- annotations(true).//
- images(false).//
- async(false).//
- projectDir(tmpResultDir).//
- addUser("admin", "admin").//
+ projectService.createProject(params.
+ authenticationToken(adminToken).
+ projectId(projectId).
+ version("").
+ complex(true).
+ projectFile(filename).
+ annotations(true).
+ images(false).
+ async(false).
+ projectDir(tmpResultDir).
+ addUser("admin", "admin").
analyzeAnnotations(true));
Project project = projectService.getProjectByProjectId(projectId, adminToken);
return project;
@@ -636,18 +636,18 @@ public class ProjectServiceTest extends ServiceTestFunctions {
}
zipFile.close();
- projectService.createProject(params.//
- authenticationToken(adminToken).//
- projectId(projectId).//
- version("").//
- complex(true).//
- projectFile(filename).//
- annotations(true).//
- images(false).//
- async(false).//
- networkLayoutAsDefault(true).//
- projectDir(tmpResultDir).//
- addUser("admin", "admin").//
+ projectService.createProject(params.
+ authenticationToken(adminToken).
+ projectId(projectId).
+ version("").
+ complex(true).
+ projectFile(filename).
+ annotations(true).
+ images(false).
+ async(false).
+ networkLayoutAsDefault(true).
+ projectDir(tmpResultDir).
+ addUser("admin", "admin").
analyzeAnnotations(true));
Project project = projectService.getProjectByProjectId(projectId, adminToken);