updated build.xml

[jalview.git] / src / jalview / io / JSONFile.java

diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java
index 5e2139e..621604c 100644 (file)
--- a/src/jalview/io/JSONFile.java
+++ b/src/jalview/io/JSONFile.java
@@ -21,6 +21,18 @@
 
 package jalview.io;
 
+import java.awt.Color;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Vector;
+
+import org.json.simple.JSONArray;
+import org.json.simple.JSONObject;
+import org.json.simple.parser.JSONParser;
+
 import jalview.api.AlignViewControllerGuiI;
 import jalview.api.AlignViewportI;
 import jalview.api.FeatureRenderer;
@@ -42,18 +54,6 @@ import jalview.json.binding.v1.SequencePojo;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
 
-import java.awt.Color;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Hashtable;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Vector;
-
-import org.json.simple.JSONArray;
-import org.json.simple.JSONObject;
-import org.json.simple.parser.JSONParser;
-
 public class JSONFile extends AlignFile
 {
   private ColourSchemeI colourScheme;
@@ -80,6 +80,10 @@ public class JSONFile extends AlignFile
 
   private JSONExportSettings jsonExportSettings;
 
+  private List<int[]> hiddenColumns;
+
+  private List<String> hiddenSeqRefs;
+
   public JSONFile()
   {
     super();
@@ -141,7 +145,7 @@ public class JSONFile extends AlignFile
         name.append(seq.getName()).append("/").append(seq.getStart())
                 .append("-").append(seq.getEnd());
         SequencePojo jsonSeqPojo = new SequencePojo();
-        jsonSeqPojo.setId(seq.getName() + "_" + seq.hashCode());
+        jsonSeqPojo.setId(String.valueOf(seq.hashCode()));
         jsonSeqPojo.setOrder(++count);
         jsonSeqPojo.setEnd(seq.getEnd());
         jsonSeqPojo.setStart(seq.getStart());
@@ -160,12 +164,18 @@ public class JSONFile extends AlignFile
                 String.valueOf(showSeqFeatures));
 
         String[] hiddenSections = exportHiddenSections();
-        if (hiddenSections != null)
+        if (hiddenSections != null && getViewport().isIncludeHiddenRegion())
         {
-          jsonAlignmentPojo.getAppSettings().put("hiddenCols",
-                  String.valueOf(hiddenSections[0]));
-          jsonAlignmentPojo.getAppSettings().put("hiddenSeqs",
-                  String.valueOf(hiddenSections[1]));
+          if (hiddenSections[0] != null)
+          {
+            jsonAlignmentPojo.getAppSettings().put("hiddenCols",
+                    String.valueOf(hiddenSections[0]));
+          }
+          if (hiddenSections[1] != null)
+          {
+            jsonAlignmentPojo.getAppSettings().put("hiddenSeqs",
+                    String.valueOf(hiddenSections[1]));
+          }
         }
       }
 
@@ -199,8 +209,7 @@ public class JSONFile extends AlignFile
           seqGrpPojo.setShowNonconserved(seqGrp.getShowNonconserved());
           for (SequenceI seq : seqGrp.getSequences())
           {
-            seqGrpPojo.getSeqsHash().add(
-                    seq.getName() + "_" + seq.hashCode());
+            seqGrpPojo.getSeqsHash().add(String.valueOf(seq.hashCode()));
           }
           jsonAlignmentPojo.getSeqGroups().add(seqGrpPojo);
         }
@@ -247,13 +256,12 @@ public class JSONFile extends AlignFile
     // hidden rows/seqs business
     HiddenSequences hiddenSeqsObj = getViewport().getAlignment()
             .getHiddenSequences();
-    if (hiddenSeqsObj == null)
+    if (hiddenSeqsObj == null || hiddenSeqsObj.hiddenSequences == null)
     {
       return hiddenSections;
     }
 
     SequenceI[] hiddenSeqs = hiddenSeqsObj.hiddenSequences;
-    System.out.print("Hidden Seqs : ");
     StringBuilder hiddenSeqsBuilder = new StringBuilder();
     for (SequenceI hiddenSeq : hiddenSeqs)
     {
@@ -267,7 +275,7 @@ public class JSONFile extends AlignFile
       hiddenSeqsBuilder.deleteCharAt(0);
     }
     hiddenSections[1] = hiddenSeqsBuilder.toString();
-    System.out.println(hiddenSections[1]);
+
     return hiddenSections;
   }
 
@@ -283,6 +291,8 @@ public class JSONFile extends AlignFile
       SequenceFeature[] seqFeatures = (dataSetSequence == null) ? null
               : seq.getDatasetSequence().getSequenceFeatures();
 
+      seqFeatures = (seqFeatures == null) ? seq.getSequenceFeatures()
+              : seqFeatures;
       if (seqFeatures == null)
       {
         continue;
@@ -294,7 +304,7 @@ public class JSONFile extends AlignFile
                 && displayedFeatures.isVisible(sf.getType()))
         {
           SequenceFeaturesPojo jsonFeature = new SequenceFeaturesPojo(
-                  seq.getName() + "_" + seq.hashCode());
+                  String.valueOf(seq.hashCode()));
           String featureColour = (fr == null) ? null : jalview.util.Format
                   .getHexString(fr
                   .findFeatureColour(Color.white, seq,
@@ -376,6 +386,8 @@ public class JSONFile extends AlignFile
                 "showSeqFeatures").toString());
         setColourScheme(getJalviewColorScheme(jsColourScheme));
         setShowSeqFeatures(showFeatures);
+        parseHiddenSeqRefsAsList(jvSettingsJsonObj);
+        parseHiddenCols(jvSettingsJsonObj);
       }
 
       seqMap = new Hashtable<String, Sequence>();
@@ -390,6 +402,10 @@ public class JSONFile extends AlignFile
         int end = Integer.valueOf(sequence.get("end").toString());
         Sequence seq = new Sequence(sequenceName, sequcenceString, start,
                 end);
+        if (hiddenSeqRefs != null && hiddenSeqRefs.contains(seqUniqueId))
+        {
+          seq.setHidden(true);
+        }
         seqs.add(seq);
         seqMap.put(seqUniqueId, seq);
       }
@@ -483,6 +499,31 @@ public class JSONFile extends AlignFile
     return this;
   }
 
+  public void parseHiddenSeqRefsAsList(JSONObject jvSettingsJson)
+  {
+    hiddenSeqRefs = new ArrayList<String>();
+    String hiddenSeqs = (String) jvSettingsJson.get("hiddenSeqs");
+    if(hiddenSeqs != null && !hiddenSeqs.isEmpty()){
+      String[] seqRefs = hiddenSeqs.split(";");
+      for(String seqRef : seqRefs){
+        hiddenSeqRefs.add(seqRef);
+      }
+    }
+  }
+
+  public void parseHiddenCols(JSONObject jvSettingsJson)
+  {
+    hiddenColumns = new ArrayList<int[]>();
+    String hiddenCols = (String) jvSettingsJson.get("hiddenCols");
+    if(hiddenCols != null && !hiddenCols.isEmpty()){
+      String[] rangeStrings = hiddenCols.split(";");
+      for(String rangeString : rangeStrings){
+        String[] range = rangeString.split("-");
+        hiddenColumns.add(new int[]
+        { Integer.valueOf(range[0]), Integer.valueOf(range[1]) });
+      }
+    }
+  }
 
   @SuppressWarnings("unchecked")
   private void parseFeatures(JSONArray jsonSeqFeatures)
@@ -543,11 +584,13 @@ public class JSONFile extends AlignFile
     return jalviewColor;
   }
 
-  public void applySettingsToAlignFrame(AlignViewControllerGuiI af)
+  public void applySettingsToAlignmentView(AlignViewControllerGuiI avc)
   {
-    af.setShowSeqFeatures(isShowSeqFeatures());
-    af.changeColour(getColourScheme());
-    af.setMenusForViewport();
+    avc.setShowSeqFeatures(isShowSeqFeatures());
+    avc.changeColour(getColourScheme());
+    avc.setMenusForViewport();
+    avc.hideColumns(hiddenColumns);
+    avc.syncHiddenSequences();
   }
 
   public String getGlobalColorScheme()
@@ -634,6 +677,11 @@ public class JSONFile extends AlignFile
     return annotations;
   }
 
+  public List<int[]> getHiddenColumns()
+  {
+    return hiddenColumns;
+  }
+
   public class JSONExportSettings
   {
     private boolean exportSequence;