X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FJSONFile.java;h=5e2139e5d3734722ae905925d27ca759a3618871;hb=e0c1dde5b241a8ac5b8c960f1f55f0940da55788;hp=8d3caddc2e73bb70465de6c6fcd8e7c165c53f5c;hpb=91c77a3db54eb4a270b03bcf9a6d97255c1fce35;p=jalview.git

diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java
index 8d3cadd..5e2139e 100644
--- a/src/jalview/io/JSONFile.java
+++ b/src/jalview/io/JSONFile.java
@@ -1,20 +1,41 @@
+/*
+ * 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.AlignViewControllerGuiI;
 import jalview.api.AlignViewportI;
 import jalview.api.FeatureRenderer;
 import jalview.api.FeaturesDisplayedI;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
+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;
@@ -37,9 +58,11 @@ public class JSONFile extends AlignFile
 {
   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";
 
@@ -129,17 +152,21 @@ public class JSONFile extends AlignFile
 
       if (jsonExportSettings.isExportJalviewSettings())
       {
-        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);
+        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 = exportHiddenSections();
+        if (hiddenSections != null)
+        {
+          jsonAlignmentPojo.getAppSettings().put("hiddenCols",
+                  String.valueOf(hiddenSections[0]));
+          jsonAlignmentPojo.getAppSettings().put("hiddenSeqs",
+                  String.valueOf(hiddenSections[1]));
+        }
       }
 
       if (jsonExportSettings.isExportAnnotations())
@@ -178,7 +205,7 @@ public class JSONFile extends AlignFile
           jsonAlignmentPojo.getSeqGroups().add(seqGrpPojo);
         }
       }
-      com.json.JSONObject generatedJSon = new com.json.JSONObject(
+      org.json.JSONObject generatedJSon = new org.json.JSONObject(
               jsonAlignmentPojo);
       jsonOutput = generatedJSon.toString();
       return jsonOutput.replaceAll("xstart", "xStart").replaceAll("xend",
@@ -190,6 +217,60 @@ public class JSONFile extends AlignFile
     return jsonOutput;
   }
 
+  public String[] exportHiddenSections()
+  {
+    String[] hiddenSections = new String[2];
+    if (getViewport() == null)
+    {
+      return null;
+    }
+
+    System.out.println("--- Hidden Sections ---");
+    // hidden column business
+    if (getViewport().hasHiddenColumns())
+    {
+      System.out.print("Hidden Cols : ");
+      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();
+      System.out.println(hiddenSections[0]);
+    }
+
+    // hidden rows/seqs business
+    HiddenSequences hiddenSeqsObj = getViewport().getAlignment()
+            .getHiddenSequences();
+    if (hiddenSeqsObj == null)
+    {
+      return hiddenSections;
+    }
+
+    SequenceI[] hiddenSeqs = hiddenSeqsObj.hiddenSequences;
+    System.out.print("Hidden Seqs : ");
+    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();
+    System.out.println(hiddenSections[1]);
+    return hiddenSections;
+  }
+
   public static List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
           List<SequenceI> seqs, FeatureRenderer fr)
   {
@@ -285,7 +366,7 @@ public class JSONFile extends AlignFile
       JSONArray seqGrpJsonArray = (JSONArray) alignmentJsonObj
               .get("seqGroups");
       JSONObject jvSettingsJsonObj = (JSONObject) alignmentJsonObj
-              .get("jalviewSettings");
+              .get("appSettings");
 
       if (jvSettingsJsonObj != null)
       {
@@ -380,7 +461,7 @@ 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();
 
@@ -462,7 +543,7 @@ public class JSONFile extends AlignFile
     return jalviewColor;
   }
 
-  public void applySettingsToAlignFrame(AlignFrame af)
+  public void applySettingsToAlignFrame(AlignViewControllerGuiI af)
   {
     af.setShowSeqFeatures(isShowSeqFeatures());
     af.changeColour(getColourScheme());
@@ -548,6 +629,11 @@ public class JSONFile extends AlignFile
     this.showSeqFeatures = showSeqFeatures;
   }
 
+  public Vector<AlignmentAnnotation> getAnnotations()
+  {
+    return annotations;
+  }
+
   public class JSONExportSettings
   {
     private boolean exportSequence;