--- /dev/null
+/*
+ * Copyright (c) 2014, Danilo Reinert (daniloreinert@growbit.com)
+ *
+ * This software is dual-licensed under:
+ *
+ * - the Lesser General Public License (LGPL) version 3.0 or, at your option, any
+ * later version;
+ * - the Apache Software License (ASL) version 2.0.
+ *
+ * The text of both licenses is available under the src/resources/ directory of
+ * this project (under the names LGPL-3.0.txt and ASL-2.0.txt respectively).
+ *
+ * Direct link to the sources:
+ *
+ * - LGPL 3.0: https://www.gnu.org/licenses/lgpl-3.0.txt
+ * - ASL 2.0: http://www.apache.org/licenses/LICENSE-2.0.txt
+ */
+
+package com.github.reinert.jjschema;
+
+import java.lang.annotation.ElementType;
+import java.lang.annotation.Retention;
+import java.lang.annotation.RetentionPolicy;
+import java.lang.annotation.Target;
+
+/**
+ * Annotation for the attributes of JSON Schema
+ *
+ * @author reinert
+ */
+@Retention(RetentionPolicy.RUNTIME)
+@Target({ElementType.METHOD, ElementType.FIELD, ElementType.TYPE})
+public @interface Attributes {
+ String $ref() default "";
+
+ String id() default "";
+
+ String title() default "";
+
+ String description() default "";
+
+ long maximum() default -1l;
+
+ boolean exclusiveMaximum() default false;
+
+ int minimum() default -1;
+
+ boolean exclusiveMinimum() default false;
+
+ String pattern() default "";
+
+ boolean required() default false;
+
+ String[] enums() default {};
+
+ int minItems() default 0;
+
+ long maxItems() default -1l;
+
+ boolean uniqueItems() default false;
+
+ int multipleOf() default 0;
+
+ int minLength() default 0;
+
+ long maxLength() default -1l;
+}
import jalview.api.AlignmentViewPanel;
import jalview.datamodel.AlignmentExportData;
import jalview.exceptions.NoFileSelectedException;
-import jalview.json.binding.v1.BioJSReleasePojo;
-import jalview.json.binding.v1.BioJSRepositoryPojo;
+import jalview.json.binding.biojs.BioJSReleasePojo;
+import jalview.json.binding.biojs.BioJSRepositoryPojo;
import jalview.util.MessageManager;
import java.io.BufferedInputStream;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
-import jalview.json.binding.v1.AlignmentAnnotationPojo;
-import jalview.json.binding.v1.AlignmentPojo;
-import jalview.json.binding.v1.AlignmentPojo.JalviewBioJsColorSchemeMapper;
-import jalview.json.binding.v1.AnnotationPojo;
-import jalview.json.binding.v1.SequenceFeaturesPojo;
-import jalview.json.binding.v1.SequenceGrpPojo;
-import jalview.json.binding.v1.SequencePojo;
+import jalview.json.binding.biojson.v1.AlignmentAnnotationPojo;
+import jalview.json.binding.biojson.v1.AlignmentPojo;
+import jalview.json.binding.biojson.v1.AnnotationPojo;
+import jalview.json.binding.biojson.v1.JalviewBioJsColorSchemeMapper;
+import jalview.json.binding.biojson.v1.SequenceFeaturesPojo;
+import jalview.json.binding.biojson.v1.SequenceGrpPojo;
+import jalview.json.binding.biojson.v1.SequencePojo;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
private ArrayList<SequenceI> hiddenSequences;
-
public JSONFile()
{
super();
parse(getReader());
}
+
@Override
public String print()
{
if (hiddenSections != null)
{
if (hiddenSections[0] != null
- && exportSettings
- .isExportHiddenColumns())
+ && exportSettings.isExportHiddenColumns())
{
jsonAlignmentPojo.getAppSettings().put("hiddenCols",
String.valueOf(hiddenSections[0]));
}
if (hiddenSections[1] != null
- && exportSettings
- .isExportHiddenSequences())
+ && exportSettings.isExportHiddenSequences())
{
jsonAlignmentPojo.getAppSettings().put("hiddenSeqs",
String.valueOf(hiddenSections[1]));
.setSeqFeatures(sequenceFeatureToJsonPojo(seqs, fr));
}
- if (exportSettings.isExportGroups()
- && seqGroups != null
+ if (exportSettings.isExportGroups() && seqGroups != null
&& seqGroups.size() > 0)
{
for (SequenceGroup seqGrp : seqGroups)
public List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
List<SequenceI> seqs, FeatureRenderer fr)
{
- displayedFeatures = (fr == null) ? null : fr
- .getFeaturesDisplayed();
+ displayedFeatures = (fr == null) ? null : fr.getFeaturesDisplayed();
List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<SequenceFeaturesPojo>();
for (SequenceI seq : seqs)
{
String.valueOf(seq.hashCode()));
String featureColour = (fr == null) ? null : jalview.util.Format
- .getHexString(fr
- .findFeatureColour(Color.white, seq,
+ .getHexString(fr.findFeatureColour(Color.white, seq,
seq.findIndex(sf.getBegin())));
jsonFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
jsonFeature.setXend(seq.findIndex(sf.getEnd()));
}
ColourSchemeI grpColourScheme = getJalviewColorScheme(colourScheme);
SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName,
- grpColourScheme,
- displayBoxes, displayText, colourText, startRes, endRes);
+ grpColourScheme, displayBoxes, displayText, colourText,
+ startRes, endRes);
seqGrp.setShowNonconserved(showNonconserved);
seqGrp.setDescription(description);
this.seqGroups.add(seqGrp);
String desc = annot.get("description") == null ? null : annot
.get("description").toString();
- char ss = annot.get("secondaryStructure") == null ? ' '
- : annot.get("secondaryStructure").toString().charAt(0);
- String displayChar = annot.get("displayCharacter").toString();
+ char ss = annot.get("secondaryStructure") == null ? ' ' : annot
+ .get("secondaryStructure").toString().charAt(0);
+ String displayChar = annot.get("displayCharacter") == null ? ""
+ : annot.get("displayCharacter").toString();
annotations[count] = new Annotation(displayChar, desc, ss, val);
}
{
hiddenSeqRefs = new ArrayList<String>();
String hiddenSeqs = (String) jvSettingsJson.get("hiddenSeqs");
- if(hiddenSeqs != null && !hiddenSeqs.isEmpty()){
+ if (hiddenSeqs != null && !hiddenSeqs.isEmpty())
+ {
String[] seqRefs = hiddenSeqs.split(";");
- for(String seqRef : seqRefs){
+ for (String seqRef : seqRefs)
+ {
hiddenSeqRefs.add(seqRef);
}
}
public void parseHiddenCols(JSONObject jvSettingsJson)
{
String hiddenCols = (String) jvSettingsJson.get("hiddenCols");
- if(hiddenCols != null && !hiddenCols.isEmpty()){
+ if (hiddenCols != null && !hiddenCols.isEmpty())
+ {
columnSelection = new ColumnSelection();
String[] rangeStrings = hiddenCols.split(";");
- for(String rangeString : rangeStrings){
+ for (String rangeString : rangeStrings)
+ {
String[] range = rangeString.split("-");
columnSelection.hideColumns(Integer.valueOf(range[0]),
Integer.valueOf(range[1]));
this.displayedFeatures = displayedFeatures;
}
-
public void configureForView(AlignmentViewPanel avpanel)
{
super.configureForView(avpanel);
{
if (hiddenSequences == null || hiddenSequences.isEmpty())
{
- return new SequenceI[]
- {};
+ return new SequenceI[] {};
}
synchronized (hiddenSequences)
{
-package jalview.json.binding.v1;
+package jalview.json.binding.biojs;
public class BioJSReleasePojo
{
-package jalview.json.binding.v1;
+package jalview.json.binding.biojs;
import java.util.ArrayList;
import java.util.Collection;
-package jalview.json.binding.v1;
+package jalview.json.binding.biojson.v1;
import java.util.ArrayList;
import java.util.List;
+import com.github.reinert.jjschema.Attributes;
+
public class AlignmentAnnotationPojo
{
+ @Attributes(required = true, description = "Serial version id for the alignAnnotation object model")
private String svid = "1.0";
+ @Attributes(required = false, description = "Label for the Alignment Annotation")
private String label;
+ @Attributes(required = false, description = "Description for the Alignment Annotation")
private String description;
+ @Attributes(required = false)
private List<AnnotationPojo> annotations = new ArrayList<AnnotationPojo>();
public String getLabel()
--- /dev/null
+package jalview.json.binding.biojson.v1;
+
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import com.github.reinert.jjschema.Attributes;
+
+@Attributes(title="BioJSON", description="A specification for the representation and exchange of bioinformatics data")
+public class AlignmentPojo
+{
+ @Attributes(required = true, description = "Serial version identifier for <b>BioJSON</b> schema")
+ private String svid = "1.0";
+
+ @Attributes(required = true, minItems = 1, maxItems = 1999999999, description = "A sequence group is a bracket of alignment residues spanning <br>across multiple columns and rows. These can be treated as a <br>sub-alignments.")
+ private List<SequencePojo> seqs = new ArrayList<SequencePojo>();
+
+ @Attributes(required = false, minItems = 0, maxItems = 1999999999, exclusiveMaximum=true, description = "Alignment annotations stores symbols and graphs usually rendered </br>below the alignment.")
+ private List<AlignmentAnnotationPojo> alignAnnotation = new ArrayList<AlignmentAnnotationPojo>();
+
+ @Attributes(required = false, minItems = 0, maxItems = 1999999999, description = "A sequence group is a bracket of alignment residues spanning <br>across multiple columns and rows. These can be treated as a <br>sub-alignments.")
+ private List<SequenceGrpPojo> seqGroups = new ArrayList<SequenceGrpPojo>();
+
+ @Attributes(required = false, minItems = 0, maxItems = 1999999999, description = "Sequence features are associated with sequences rather than <br>alignments. A sequence feature can span across multiple <br>sequences in an alignment. They indicate features generated <br>by the same analysis process or retrieved from the same database <br>(such as Uniprot features).")
+ private List<SequenceFeaturesPojo> seqFeatures = new ArrayList<SequenceFeaturesPojo>();
+
+ @Attributes(required = false, enums = { "None", "Custom", "Clustal",
+ "Zappo", "Taylor", "Nucleotide", "Pyrimidine", "Purine", "Turn",
+ "Strand", "Buried", "Hydro" })
+ private String colourScheme;
+
+ @Attributes(required = true, maxItems = 1, description = "This is an array of key=value pairs for storing custom application <br>specific settings")
+ Map<String, Object> appSettings = new HashMap<String, Object>();
+
+ public AlignmentPojo()
+ {
+ }
+
+ public List<SequencePojo> getSeqs()
+ {
+ return seqs;
+ }
+
+ public void setSeqs(ArrayList<SequencePojo> seqs)
+ {
+ this.seqs = seqs;
+ }
+
+ public Map<String, Object> getAppSettings()
+ {
+ return appSettings;
+ }
+
+ public void setAppSettings(Map<String, Object> appSettings)
+ {
+ this.appSettings = appSettings;
+ }
+
+ public List<AlignmentAnnotationPojo> getAlignAnnotation()
+ {
+ return alignAnnotation;
+ }
+
+ public void setAlignAnnotation(
+ List<AlignmentAnnotationPojo> alignAnnotation)
+ {
+ this.alignAnnotation = alignAnnotation;
+ }
+
+ public List<SequenceGrpPojo> getSeqGroups()
+ {
+ return seqGroups;
+ }
+
+ public void setSeqGroups(List<SequenceGrpPojo> seqGroups)
+ {
+ this.seqGroups = seqGroups;
+ }
+
+ public List<SequenceFeaturesPojo> getSeqFeatures()
+ {
+ return seqFeatures;
+ }
+
+ public void setSeqFeatures(List<SequenceFeaturesPojo> seqFeatures)
+ {
+ this.seqFeatures = seqFeatures;
+ }
+
+ public String getSvid()
+ {
+ return svid;
+ }
+
+ public void setGlobalColorScheme(String globalColorScheme)
+ {
+// this.appSettings.put("globalColorScheme", globalColorScheme);
+ }
+
+ public String getColourScheme()
+ {
+ return colourScheme;
+ }
+
+ public void setColourScheme(String colourScheme)
+ {
+ this.colourScheme = colourScheme;
+ }
+
+}
--- /dev/null
+package jalview.json.binding.biojson.v1;
+
+import com.github.reinert.jjschema.Attributes;
+
+public class AnnotationPojo
+{
+ @Attributes(required = false, description = "Display character for the given annotation")
+ private String displayCharacter;
+
+ @Attributes(required = false, description = "Description for the annotation")
+ private String description;
+
+ @Attributes(required = true, enums = {"E", "H", "\u0000", ")", "("}, description = "Determines what is rendered for the secondary </br>structure <ul><li>’E’ - indicates Beta Sheet/Strand <li>’H’ - indicates alpha helix </li><li> ‘\\u0000’ - indicates blank</li></ul></br>For RNA Helix (only shown when working with</br> nucleotide sequences): <ul><li> ‘(’ - indicates bases pair with columns upstream</br> (to right) </li><li> ’(’ - indicate region pairs with bases to the left</li></ul>")
+ private char secondaryStructure;
+
+ @Attributes(required = false, description = "Value of the annotation")
+ private float value;
+
+
+ public String getDisplayCharacter()
+ {
+ return displayCharacter;
+ }
+
+ public void setDisplayCharacter(String displayCharacter)
+ {
+ this.displayCharacter = displayCharacter;
+ }
+
+ public String getDescription()
+ {
+ return description;
+ }
+
+ public void setDescription(String description)
+ {
+ this.description = description;
+ }
+
+ public char getSecondaryStructure()
+ {
+ return secondaryStructure;
+ }
+
+ public void setSecondaryStructure(char secondaryStructure)
+ {
+ this.secondaryStructure = secondaryStructure;
+ }
+
+ public float getValue()
+ {
+ return value;
+ }
+
+ public void setValue(float value)
+ {
+ this.value = value;
+ }
+
+}
-package jalview.json.binding.v1;
+package jalview.json.binding.biojson.v1;
public class AppSettingsPojo
--- /dev/null
+package jalview.json.binding.biojson.v1;
+
+import jalview.schemes.Blosum62ColourScheme;
+import jalview.schemes.BuriedColourScheme;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.HelixColourScheme;
+import jalview.schemes.HydrophobicColourScheme;
+import jalview.schemes.NucleotideColourScheme;
+import jalview.schemes.PIDColourScheme;
+import jalview.schemes.PurinePyrimidineColourScheme;
+import jalview.schemes.RNAInteractionColourScheme;
+import jalview.schemes.StrandColourScheme;
+import jalview.schemes.TaylorColourScheme;
+import jalview.schemes.TurnColourScheme;
+import jalview.schemes.ZappoColourScheme;
+
+public enum JalviewBioJsColorSchemeMapper
+{
+
+ USER_DEFINED("User Defined", "user defined", null), NONE("None", "foo",
+ null), CLUSTAL("Clustal", "clustal", null), ZAPPO("Zappo",
+ "zappo", new ZappoColourScheme()), TAYLOR("Taylor", "taylor",
+ new TaylorColourScheme()), NUCLEOTIDE("Nucleotide", "nucleotide",
+ new NucleotideColourScheme()), PURINE_PYRIMIDINE(
+ "Purine/Pyrimidine", "purine", new PurinePyrimidineColourScheme()), HELIX_PROPENCITY(
+ "Helix Propensity", "helix", new HelixColourScheme()), TURN_PROPENSITY(
+ "Turn Propensity", "turn", new TurnColourScheme()), STRAND_PROPENSITY(
+ "Strand Propensity", "strand", new StrandColourScheme()), BURIED_INDEX(
+ "Buried Index", "buried", new BuriedColourScheme()), HYDROPHOBIC(
+ "Hydrophobic", "hydro", new HydrophobicColourScheme()),
+
+ // The color types below are not yet supported by BioJs MSA viewer
+ T_COFFE_SCORES("T-Coffee Scores", "T-Coffee Scores", null), RNA_INT_TYPE(
+ "RNA Interaction type", "RNA Interaction type",
+ new RNAInteractionColourScheme()), BLOSUM62("Blosum62",
+ "Blosum62", new Blosum62ColourScheme()), RNA_HELICES(
+ "RNA Helices", "RNA Helices", null), PERCENTAGE_IDENTITY(
+ "% Identity", "pid", new PIDColourScheme());
+
+ private String jalviewName;
+
+ private String bioJsName;
+
+ private ColourSchemeI jvColourScheme;
+
+ private JalviewBioJsColorSchemeMapper(String jalviewName,
+ String bioJsName, ColourSchemeI jvColourScheme)
+ {
+ this.jalviewName = jalviewName;
+ this.bioJsName = bioJsName;
+ this.setJvColourScheme(jvColourScheme);
+ }
+
+ public String getJalviewName()
+ {
+ return jalviewName;
+ }
+
+ public String getBioJsName()
+ {
+ return bioJsName;
+ }
+
+ public ColourSchemeI getJvColourScheme()
+ {
+ return jvColourScheme;
+ }
+
+ public void setJvColourScheme(ColourSchemeI jvColourScheme)
+ {
+ this.jvColourScheme = jvColourScheme;
+ }
+
+}
-package jalview.json.binding.v1;
+package jalview.json.binding.biojson.v1;
-import java.util.Hashtable;
+import java.util.Map;
import java.util.Vector;
+import com.github.reinert.jjschema.Attributes;
+
public class SequenceFeaturesPojo
{
+ @Attributes(required = true, description = "Serial version id for the <b>SeqFeature</b> object")
private String svid = "1.0";
- private int xstart;
+ @Attributes(required = true, description = "Start residue position for the sequence feature")
+ private int xStart;
- private int xend;
+ @Attributes(required = true, description = "End residue position for the sequence feature")
+ private int xEnd;
+ @Attributes(required = true, minItems = 1, maxItems = 1999999999, description = "Reference to the sequence in the alignment<br> (more like a foreign key)")
private String sequenceRef;
+ @Attributes(required = true, description = "The name or type of the SequenceFeature")
private String type;
+ @Attributes(required = false, description = "Score")
private Float score;
+ @Attributes(required = false, description = "Description for the feature")
private String description;
+
+ @Attributes(required = false, description = "Additional metadata for the feature")
+ private Map<String, Object> otherDetails;
- private Hashtable otherDetails;
-
+ @Attributes(required = false, description = "Fill colour")
private String fillColor;
+ @Attributes(required = true, description = "Feature group")
private String featureGroup;
+ @Attributes(required = false, description = "URL links associated to the feature")
private Vector<String> links;
public SequenceFeaturesPojo()
public int getXstart()
{
- return xstart;
+ return xStart;
}
- public void setXstart(int xstart)
+ public void setXstart(int xStart)
{
- this.xstart = xstart;
+ this.xStart = xStart;
}
public int getXend()
{
- return xend;
+ return xEnd;
}
public void setXend(int xend)
{
- this.xend = xend;
+ this.xEnd = xend;
}
public String getType()
this.description = description;
}
- public Hashtable getOtherDetails()
+ public Map<String, Object> getOtherDetails()
{
return otherDetails;
}
- public void setOtherDetails(Hashtable otherDetails)
+ public void setOtherDetails(Map<String, Object> otherDetails)
{
this.otherDetails = otherDetails;
}
return svid;
}
+//public Map<String, Object> getOtherDetails() {
+// return otherDetails;
+//}
+//
+//public void setOtherDetails(Map<String, Object> otherDetails) {
+// this.otherDetails = otherDetails;
+//}
+
}
-package jalview.json.binding.v1;
+package jalview.json.binding.biojson.v1;
import java.util.ArrayList;
+import com.github.reinert.jjschema.Attributes;
+
public class SequenceGrpPojo
{
+ @Attributes(required = true, description = "Serial version identifier for the <b>seqGroup</b> object model")
private String svid = "1.0";
-
+
+ @Attributes(required = false, description = "The Colour Scheme applied to the Sequence Group")
private String colourScheme;
+ @Attributes(required = true, description = "The name assigned to the seqGroup")
private String groupName;
+ @Attributes(required = false, description = "Serial version identifier for the <b>seqGroup</b> object model")
private String description;
+ @Attributes(required = false, description = "Determines if the seqGroup border should be visible or not")
private boolean displayBoxes;
+ @Attributes(required = false, description = "Determines if the texts of the group is displayed or not")
private boolean displayText;
+ @Attributes(required = false, description = "Determines if the residues text for the group is coloured")
private boolean colourText;
+ @Attributes(required = false, description = "Boolean value indicating whether residues should only be shown <br/>that are different from current reference or consensus sequence")
private boolean showNonconserved;
+ @Attributes(required = true, description = "The index of the group’s first residue in the alignment space")
private int startRes;
+ @Attributes(required = true, description = "The index of the group’s last residue in the alignment space")
private int endRes;
-
+
+ @Attributes(required = true, minItems = 1, maxItems = 1999999999, uniqueItems=true, description = "An array of the unique id's for the sequences belonging to the group")
private ArrayList<String> sequenceRefs = new ArrayList<String>();
public String getColourScheme()
-package jalview.json.binding.v1;
+package jalview.json.binding.biojson.v1;
+
+import com.github.reinert.jjschema.Attributes;
public class SequencePojo
{
+ @Attributes(required = true, description = "Serial version identifier for the <b>seqs</b> object model")
private String svid = "1.0";
+ @Attributes(required = true,minLength=3,maxLength=1999999999, description = "Sequence residue characters. An aligned sequence may contain <br>one of the following gap characters “.”, “-” or “ ”")
private String seq;
+ @Attributes(required = true, description = "Sequence name")
private String name;
+ @Attributes(required = false, description = "Sequence type", enums = {"DNA", "RNA", "Protein"})
private String type;
+ @Attributes(required = true, description = "Unique identifier for a given Sequence")
private String id;
-
+
+ @Attributes(required = false, description = "The order/position of a sequence in the alignment space")
private int order;
-
+
+ @Attributes(required = true, description = "The index of the sequence’s first residue in its source database, <br>using a one-based numbering index system")
private int start;
+ @Attributes(required = true, description = "The index of the sequence’s last residue in its source database, <br>using a one-based numbering index system")
private int end;
+++ /dev/null
-package jalview.json.binding.v1;
-
-import jalview.schemes.Blosum62ColourScheme;
-import jalview.schemes.BuriedColourScheme;
-import jalview.schemes.ColourSchemeI;
-import jalview.schemes.HelixColourScheme;
-import jalview.schemes.HydrophobicColourScheme;
-import jalview.schemes.NucleotideColourScheme;
-import jalview.schemes.PIDColourScheme;
-import jalview.schemes.PurinePyrimidineColourScheme;
-import jalview.schemes.RNAInteractionColourScheme;
-import jalview.schemes.StrandColourScheme;
-import jalview.schemes.TaylorColourScheme;
-import jalview.schemes.TurnColourScheme;
-import jalview.schemes.ZappoColourScheme;
-
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-
-public class AlignmentPojo
-{
- private String svid = "1.0";
-
- private List<SequencePojo> seqs = new ArrayList<SequencePojo>();
-
- private List<AlignmentAnnotationPojo> alignAnnotation = new ArrayList<AlignmentAnnotationPojo>();
-
- private List<SequenceGrpPojo> seqGroups = new ArrayList<SequenceGrpPojo>();
-
- private List<SequenceFeaturesPojo> seqFeatures = new ArrayList<SequenceFeaturesPojo>();
-
- HashMap<String, String> appSettings = new HashMap<String, String>();
-
- public AlignmentPojo()
- {
- }
-
- public List<SequencePojo> getSeqs()
- {
- return seqs;
- }
-
- public void setSeqs(ArrayList<SequencePojo> seqs)
- {
- this.seqs = seqs;
- }
-
- public HashMap<String, String> getAppSettings()
- {
- return appSettings;
- }
-
- public void setAppSettings(HashMap<String, String> appSettings)
- {
- this.appSettings = appSettings;
- }
-
- public List<AlignmentAnnotationPojo> getAlignAnnotation()
- {
- return alignAnnotation;
- }
-
- public void setAlignAnnotation(
- List<AlignmentAnnotationPojo> alignAnnotation)
- {
- this.alignAnnotation = alignAnnotation;
- }
-
- public List<SequenceGrpPojo> getSeqGroups()
- {
- return seqGroups;
- }
-
- public void setSeqGroups(List<SequenceGrpPojo> seqGroups)
- {
- this.seqGroups = seqGroups;
- }
-
- public List<SequenceFeaturesPojo> getSeqFeatures()
- {
- return seqFeatures;
- }
-
- public void setSeqFeatures(List<SequenceFeaturesPojo> seqFeatures)
- {
- this.seqFeatures = seqFeatures;
- }
-
- public String getSvid()
- {
- return svid;
- }
-
- public void setGlobalColorScheme(String globalColorScheme)
- {
- for (JalviewBioJsColorSchemeMapper cs : JalviewBioJsColorSchemeMapper
- .values())
- {
- if (cs.getJalviewName().equals(globalColorScheme))
- {
- // this.globalColorScheme = cs.getBioJsName();
- this.appSettings.put("globalColorScheme", cs.getBioJsName());
- break;
- }
- }
- }
-
- public enum JalviewBioJsColorSchemeMapper
- {
- USER_DEFINED("User Defined", "user defined", null), NONE("None", "foo",
- null), CLUSTAL("Clustal", "clustal", null), ZAPPO("Zappo",
- "zappo", new ZappoColourScheme()), TAYLOR("Taylor", "taylor",
- new TaylorColourScheme()), NUCLEOTIDE("Nucleotide",
- "nucleotide", new NucleotideColourScheme()), PURINE_PYRIMIDINE(
- "Purine/Pyrimidine", "purine",
- new PurinePyrimidineColourScheme()), HELIX_PROPENCITY(
- "Helix Propensity", "helix", new HelixColourScheme()), TURN_PROPENSITY(
- "Turn Propensity", "turn", new TurnColourScheme()), STRAND_PROPENSITY(
- "Strand Propensity", "strand", new StrandColourScheme()), BURIED_INDEX(
- "Buried Index", "buried", new BuriedColourScheme()), HYDROPHOBIC(
- "Hydrophobic", "hydro", new HydrophobicColourScheme()),
-
- // The color types below are not yet supported by BioJs MSA viewer
- T_COFFE_SCORES("T-Coffee Scores", "T-Coffee Scores", null), RNA_INT_TYPE(
- "RNA Interaction type", "RNA Interaction type",
- new RNAInteractionColourScheme()), BLOSUM62("Blosum62",
- "Blosum62", new Blosum62ColourScheme()), RNA_HELICES(
- "RNA Helices", "RNA Helices", null), PERCENTAGE_IDENTITY(
- "% Identity", "pid", new PIDColourScheme());
-
- private String jalviewName;
-
- private String bioJsName;
-
- private ColourSchemeI jvColourScheme;
-
- private JalviewBioJsColorSchemeMapper(String jalviewName,
- String bioJsName, ColourSchemeI jvColourScheme)
- {
- this.jalviewName = jalviewName;
- this.bioJsName = bioJsName;
- this.setJvColourScheme(jvColourScheme);
- }
-
- public String getJalviewName()
- {
- return jalviewName;
- }
-
- public String getBioJsName()
- {
- return bioJsName;
- }
-
- public ColourSchemeI getJvColourScheme()
- {
- return jvColourScheme;
- }
-
- public void setJvColourScheme(ColourSchemeI jvColourScheme)
- {
- this.jvColourScheme = jvColourScheme;
- }
-
- }
-
-}
+++ /dev/null
-package jalview.json.binding.v1;
-
-
-public class AnnotationPojo
-{
- private String displayCharacter = "";
-
- private String description;
-
- private char secondaryStructure;
-
- private float value;
-
-
- public String getDisplayCharacter()
- {
- return displayCharacter;
- }
-
- public void setDisplayCharacter(String displayCharacter)
- {
- this.displayCharacter = displayCharacter;
- }
-
- public String getDescription()
- {
- return description;
- }
-
- public void setDescription(String description)
- {
- this.description = description;
- }
-
- public char getSecondaryStructure()
- {
- return secondaryStructure;
- }
-
- public void setSecondaryStructure(char secondaryStructure)
- {
- this.secondaryStructure = secondaryStructure;
- }
-
- public float getValue()
- {
- return value;
- }
-
- public void setValue(float value)
- {
- this.value = value;
- }
-
-}
package jalview.io;
-import jalview.json.binding.v1.BioJSReleasePojo;
-import jalview.json.binding.v1.BioJSRepositoryPojo;
+import jalview.json.binding.biojs.BioJSReleasePojo;
+import jalview.json.binding.biojs.BioJSRepositoryPojo;
import java.io.File;
import java.io.IOException;
git://source.jalview.org / jalview.git / commitdiff