X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FJSONFile.java;h=bbbc122e2b8666d97819ba8f998785e2a8c7955a;hb=93d63f3c608771bb48b5ac18f761194a1ea28554;hp=28b8ed22f1b877de07fededa54487a21e0b022f2;hpb=7ce1382b998c007a78c9b33a3dc331e966eebc4b;p=jalview.git

diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java
index 28b8ed2..bbbc122 100644
--- a/src/jalview/io/JSONFile.java
+++ b/src/jalview/io/JSONFile.java
@@ -1,20 +1,42 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+
 package jalview.io;
 
 import jalview.api.AlignViewportI;
+import jalview.api.ComplexAlignFile;
 import jalview.api.FeatureRenderer;
 import jalview.api.FeaturesDisplayedI;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenSequences;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
-import jalview.gui.AlignFrame;
 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.JalviewSettingsPojo;
-import jalview.json.binding.v1.JalviewSettingsPojo.JalviewBioJsColorSchemeMapper;
 import jalview.json.binding.v1.SequenceFeaturesPojo;
 import jalview.json.binding.v1.SequenceGrpPojo;
 import jalview.json.binding.v1.SequencePojo;
@@ -23,6 +45,7 @@ import jalview.schemes.ColourSchemeProperty;
 
 import java.awt.Color;
 import java.io.IOException;
+import java.io.Reader;
 import java.util.ArrayList;
 import java.util.Hashtable;
 import java.util.Iterator;
@@ -33,13 +56,15 @@ import org.json.simple.JSONArray;
 import org.json.simple.JSONObject;
 import org.json.simple.parser.JSONParser;
 
-public class JSONFile extends AlignFile
+public class JSONFile extends AlignFile implements ComplexAlignFile
 {
   private ColourSchemeI colourScheme;
 
-  private String jalviewVersion;
+  private String version = "2.9";
+
+  private String webstartUrl = "www.jalview.org/services/launchApp";
 
-  private String webStartLaunchServletUrl;
+  private String application = "Jalview";
 
   public static final String FILE_EXT = "json";
 
@@ -55,7 +80,13 @@ public class JSONFile extends AlignFile
 
   private FeatureRenderer fr;
 
-  private JSONExportSettings jsonExportSettings;
+  private List<int[]> hiddenColumns;
+
+  private ColumnSelection columnSelection;
+
+  private List<String> hiddenSeqRefs;
+
+  private ArrayList<SequenceI> hiddenSequences;
 
   public JSONFile()
   {
@@ -75,30 +106,16 @@ public class JSONFile extends AlignFile
   @Override
   public void parse() throws IOException
   {
-    StringBuilder jsonStringBuilder = new StringBuilder();
-    String currentLine;
-    while ((currentLine = nextLine()) != null)
-    {
-      jsonStringBuilder.append(currentLine);
-    }
-    parse(jsonStringBuilder.toString());
+    parse(getReader());
 
   }
 
   @Override
   public String print()
   {
+    String jsonOutput = null;
     try
     {
-      if (getJsonExportSettings() == null)
-      {
-        jsonExportSettings = new JSONExportSettings();
-        jsonExportSettings.setExportAnnotations(true);
-        jsonExportSettings.setExportGroups(true);
-        jsonExportSettings.setExportJalviewSettings(true);
-        jsonExportSettings.setExportSequenceFeatures(true);
-      }
-
       AlignmentPojo jsonAlignmentPojo = new AlignmentPojo();
       if (getViewport() != null)
       {
@@ -117,7 +134,7 @@ 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());
@@ -126,34 +143,46 @@ public class JSONFile extends AlignFile
         jsonAlignmentPojo.getSeqs().add(jsonSeqPojo);
       }
 
-      if (jsonExportSettings.isExportJalviewSettings())
+      jsonAlignmentPojo.setGlobalColorScheme(globalColorScheme);
+      jsonAlignmentPojo.getAppSettings().put("application", application);
+      jsonAlignmentPojo.getAppSettings().put("version", version);
+      jsonAlignmentPojo.getAppSettings().put("webStartUrl", webstartUrl);
+      jsonAlignmentPojo.getAppSettings().put("showSeqFeatures",
+              String.valueOf(showSeqFeatures));
+
+      String[] hiddenSections = getHiddenSections();
+      if (hiddenSections != null)
       {
-        jalviewVersion = jalview.bin.Cache.getProperty("VERSION");
-        webStartLaunchServletUrl = jalview.bin.Cache.getDefault(
-                "www.jalview.org", "http://www.jalview.org")
-                + "/services/launchApp";
-
-        JalviewSettingsPojo jvSettings = new JalviewSettingsPojo();
-        jvSettings.setGlobalColorScheme(globalColorScheme);
-        jvSettings.setJalviewVersion(jalviewVersion);
-        jvSettings.setWebStartUrl(webStartLaunchServletUrl);
-        jvSettings.setShowSeqFeatures(showSeqFeatures);
-        jsonAlignmentPojo.setJalviewSettings(jvSettings);
+        if (hiddenSections[0] != null
+                && getViewport().getExportSettings()
+                        .isExportHiddenColumns())
+        {
+          jsonAlignmentPojo.getAppSettings().put("hiddenCols",
+                  String.valueOf(hiddenSections[0]));
+        }
+        if (hiddenSections[1] != null
+                && getViewport().getExportSettings()
+                        .isExportHiddenSequences())
+        {
+          jsonAlignmentPojo.getAppSettings().put("hiddenSeqs",
+                  String.valueOf(hiddenSections[1]));
+        }
       }
 
-      if (jsonExportSettings.isExportAnnotations())
+      if (getViewport().getExportSettings().isExportAnnotations())
       {
         jsonAlignmentPojo
                 .setAlignAnnotation(annotationToJsonPojo(annotations));
       }
 
-      if (jsonExportSettings.isExportSequenceFeatures())
+      if (getViewport().getExportSettings().isExportFeatures())
       {
         jsonAlignmentPojo
                 .setSeqFeatures(sequenceFeatureToJsonPojo(seqs, fr));
       }
 
-      if (jsonExportSettings.isExportGroups() && seqGroups != null
+      if (getViewport().getExportSettings().isExportGroups()
+              && seqGroups != null
               && seqGroups.size() > 0)
       {
         for (SequenceGroup seqGrp : seqGroups)
@@ -171,22 +200,71 @@ 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);
         }
       }
-      com.json.JSONObject generatedJSon = new com.json.JSONObject(
+      org.json.JSONObject generatedJSon = new org.json.JSONObject(
               jsonAlignmentPojo);
-      String jsonOutput = generatedJSon.toString();
+      jsonOutput = generatedJSon.toString();
       return jsonOutput.replaceAll("xstart", "xStart").replaceAll("xend",
               "xEnd");
     } catch (Exception e)
     {
       e.printStackTrace();
-      throw e;
     }
+    return jsonOutput;
+  }
+
+  public String[] getHiddenSections()
+  {
+    String[] hiddenSections = new String[2];
+    if (getViewport() == null)
+    {
+      return null;
+    }
+
+    // hidden column business
+    if (getViewport().hasHiddenColumns())
+    {
+      List<int[]> hiddenCols = getViewport().getColumnSelection()
+              .getHiddenColumns();
+      StringBuilder hiddenColsBuilder = new StringBuilder();
+      for (int[] range : hiddenCols)
+      {
+        hiddenColsBuilder.append(";").append(range[0]).append("-")
+                .append(range[1]);
+      }
+
+      hiddenColsBuilder.deleteCharAt(0);
+      hiddenSections[0] = hiddenColsBuilder.toString();
+    }
+
+    // hidden rows/seqs business
+    HiddenSequences hiddenSeqsObj = getViewport().getAlignment()
+            .getHiddenSequences();
+    if (hiddenSeqsObj == null || hiddenSeqsObj.hiddenSequences == null)
+    {
+      return hiddenSections;
+    }
+
+    SequenceI[] hiddenSeqs = hiddenSeqsObj.hiddenSequences;
+    StringBuilder hiddenSeqsBuilder = new StringBuilder();
+    for (SequenceI hiddenSeq : hiddenSeqs)
+    {
+      if (hiddenSeq != null)
+      {
+        hiddenSeqsBuilder.append(";").append(hiddenSeq.hashCode());
+      }
+    }
+    if (hiddenSeqsBuilder.length() > 0)
+    {
+      hiddenSeqsBuilder.deleteCharAt(0);
+    }
+    hiddenSections[1] = hiddenSeqsBuilder.toString();
+
+    return hiddenSections;
   }
 
   public static List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
@@ -201,6 +279,8 @@ public class JSONFile extends AlignFile
       SequenceFeature[] seqFeatures = (dataSetSequence == null) ? null
               : seq.getDatasetSequence().getSequenceFeatures();
 
+      seqFeatures = (seqFeatures == null) ? seq.getSequenceFeatures()
+              : seqFeatures;
       if (seqFeatures == null)
       {
         continue;
@@ -212,7 +292,7 @@ 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,
@@ -269,7 +349,7 @@ public class JSONFile extends AlignFile
   }
 
   @SuppressWarnings("unchecked")
-  public JSONFile parse(String jsonAlignmentString)
+  public JSONFile parse(Reader jsonAlignmentString)
   {
     try
     {
@@ -284,7 +364,7 @@ public class JSONFile extends AlignFile
       JSONArray seqGrpJsonArray = (JSONArray) alignmentJsonObj
               .get("seqGroups");
       JSONObject jvSettingsJsonObj = (JSONObject) alignmentJsonObj
-              .get("jalviewSettings");
+              .get("appSettings");
 
       if (jvSettingsJsonObj != null)
       {
@@ -294,8 +374,11 @@ public class JSONFile extends AlignFile
                 "showSeqFeatures").toString());
         setColourScheme(getJalviewColorScheme(jsColourScheme));
         setShowSeqFeatures(showFeatures);
+        parseHiddenSeqRefsAsList(jvSettingsJsonObj);
+        parseHiddenCols(jvSettingsJsonObj);
       }
 
+      hiddenSequences = new ArrayList<SequenceI>();
       seqMap = new Hashtable<String, Sequence>();
       for (Iterator<JSONObject> sequenceIter = seqJsonArray.iterator(); sequenceIter
               .hasNext();)
@@ -308,6 +391,10 @@ 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))
+        {
+          hiddenSequences.add(seq);
+        }
         seqs.add(seq);
         seqMap.put(seqUniqueId, seq);
       }
@@ -379,7 +466,7 @@ public class JSONFile extends AlignFile
             String desc = annot.get("description") == null ? null : annot
                     .get("description").toString();
 
-            char ss = annot.get("secondaryStructure") == null ? null
+            char ss = annot.get("secondaryStructure") == null ? ' '
                     : annot.get("secondaryStructure").toString().charAt(0);
             String displayChar = annot.get("displayCharacter").toString();
 
@@ -401,6 +488,31 @@ 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)
+  {
+    String hiddenCols = (String) jvSettingsJson.get("hiddenCols");
+    if(hiddenCols != null && !hiddenCols.isEmpty()){
+      columnSelection = new ColumnSelection();
+      String[] rangeStrings = hiddenCols.split(";");
+      for(String rangeString : rangeStrings){
+        String[] range = rangeString.split("-");
+        columnSelection.hideColumns(Integer.valueOf(range[0]),
+                Integer.valueOf(range[1]));
+      }
+    }
+  }
 
   @SuppressWarnings("unchecked")
   private void parseFeatures(JSONArray jsonSeqFeatures)
@@ -418,9 +530,6 @@ public class JSONFile extends AlignFile
         String descripiton = (String) jsonFeature.get("description");
         String seqRef = (String) jsonFeature.get("sequenceRef");
         Float score = Float.valueOf(jsonFeature.get("score").toString());
-        // Hashtable otherDetails = (Hashtable) jsonFeature
-        // .get("otherDetails");
-        // sequenceFeature.otherDetails = otherDetails;
 
         Sequence seq = seqMap.get(seqRef);
         SequenceFeature sequenceFeature = new SequenceFeature();
@@ -461,13 +570,6 @@ public class JSONFile extends AlignFile
     return jalviewColor;
   }
 
-  public void applySettingsToAlignFrame(AlignFrame af)
-  {
-    af.setShowSeqFeatures(isShowSeqFeatures());
-    af.changeColour(getColourScheme());
-    af.setMenusForViewport();
-  }
-
   public String getGlobalColorScheme()
   {
     return globalColorScheme;
@@ -498,15 +600,6 @@ public class JSONFile extends AlignFile
     this.displayedFeatures = displayedFeatures;
   }
 
-  public JSONExportSettings getJsonExportSettings()
-  {
-    return jsonExportSettings;
-  }
-
-  public void setJsonExportSettings(JSONExportSettings jsonExportSettings)
-  {
-    this.jsonExportSettings = jsonExportSettings;
-  }
 
   public static String getJSONData(AlignViewportI av)
   {
@@ -547,6 +640,44 @@ public class JSONFile extends AlignFile
     this.showSeqFeatures = showSeqFeatures;
   }
 
+  public Vector<AlignmentAnnotation> getAnnotations()
+  {
+    return annotations;
+  }
+
+  public List<int[]> getHiddenColumns()
+  {
+    return hiddenColumns;
+  }
+
+  public ColumnSelection getColumnSelection()
+  {
+    return columnSelection;
+  }
+
+  public void setColumnSelection(ColumnSelection columnSelection)
+  {
+    this.columnSelection = columnSelection;
+  }
+
+  public SequenceI[] getHiddenSequences()
+  {
+    if (hiddenSequences == null || hiddenSequences.isEmpty())
+    {
+      return new SequenceI[]
+      {};
+    }
+    synchronized (hiddenSequences)
+    {
+      return hiddenSequences.toArray(new SequenceI[hiddenSequences.size()]);
+    }
+  }
+
+  public void setHiddenSequences(ArrayList<SequenceI> hiddenSequences)
+  {
+    this.hiddenSequences = hiddenSequences;
+  }
+
   public class JSONExportSettings
   {
     private boolean exportSequence;