Merge branch 'Release_2_7_Branch' into develop

[jalview.git] / src / jalview / gui / Jalview2XML.java

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 3c5259e..6d55c32 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -38,6 +38,7 @@ import jalview.datamodel.SequenceI;
 import jalview.schemabinding.version2.*;
 import jalview.schemes.*;
 import jalview.structure.StructureSelectionManager;
+import jalview.util.Platform;
 import jalview.util.jarInputStreamProvider;
 
 /**
@@ -426,9 +427,9 @@ public class Jalview2XML
     object.setCreationDate(new java.util.Date(System.currentTimeMillis()));
     object.setVersion(jalview.bin.Cache.getProperty("VERSION"));
 
-    jalview.datamodel.AlignmentI jal = av.alignment;
+    jalview.datamodel.AlignmentI jal = av.getAlignment();
 
-    if (av.hasHiddenRows)
+    if (av.hasHiddenRows())
     {
       jal = jal.getHiddenSequences().getFullAlignment();
     }
@@ -497,15 +498,13 @@ public class Jalview2XML
 
       jseq.setId(id); // jseq id should be a string not a number
 
-      if (av.hasHiddenRows)
+      if (av.hasHiddenRows())
       {
-        jseq.setHidden(av.alignment.getHiddenSequences().isHidden(jds));
+        jseq.setHidden(av.getAlignment().getHiddenSequences().isHidden(jds));
 
-        if (av.hiddenRepSequences != null
-                && av.hiddenRepSequences.containsKey(jal.getSequenceAt(i)))
+        if (av.isHiddenRepSequence(jal.getSequenceAt(i)))
         {
-          jalview.datamodel.SequenceI[] reps = ((jalview.datamodel.SequenceGroup) av.hiddenRepSequences
-                  .get(jal.getSequenceAt(i))).getSequencesInOrder(jal);
+          jalview.datamodel.SequenceI[] reps = av.getRepresentedSequences(jal.getSequenceAt(i)).getSequencesInOrder(jal);
 
           for (int h = 0; h < reps.length; h++)
           {
@@ -707,9 +706,9 @@ public class Jalview2XML
       jms.addJSeq(jseq);
     }
 
-    if (av.hasHiddenRows)
+    if (av.hasHiddenRows())
     {
-      jal = av.alignment;
+      jal = av.getAlignment();
     }
     // SAVE MAPPINGS
     if (jal.getCodonFrames() != null && jal.getCodonFrames().length > 0)
@@ -765,7 +764,7 @@ public class Jalview2XML
           {
             TreePanel tp = (TreePanel) frames[t];
 
-            if (tp.treeCanvas.av.alignment == jal)
+            if (tp.treeCanvas.av.getAlignment() == jal)
             {
               Tree tree = new Tree();
               tree.setTitle(tp.getTitle());
@@ -865,8 +864,8 @@ public class Jalview2XML
 
         an.setLabel(aa[i].label);
 
-        if (aa[i] == av.quality || aa[i] == av.conservation
-                || aa[i] == av.consensus || aa[i].autoCalculated)
+        if (aa[i] == av.getAlignmentQualityAnnot() || aa[i] == av.getAlignmentConservationAnnotation()
+                || aa[i] == av.getAlignmentConsensusAnnotation() || aa[i].autoCalculated)
         {
           // new way of indicating autocalculated annotation -
           an.setAutoCalculated(aa[i].autoCalculated);
@@ -1205,7 +1204,7 @@ public class Jalview2XML
 
     }
 
-    if (av.hasHiddenColumns)
+    if (av.hasHiddenColumns())
     {
       if (av.getColumnSelection() == null
               || av.getColumnSelection().getHiddenColumns() == null)
@@ -1823,7 +1822,7 @@ public class Jalview2XML
         }
         ;
         out.close();
-        String t=outFile.toURI().getPath().substring(1);
+        String t=outFile.getAbsolutePath();
         alreadyLoadedPDB.put(pdbId, t);
         return t;
       }
@@ -2730,6 +2729,8 @@ public class Jalview2XML
               {
                 newFileLoc = new StringBuffer();
               }
+              do {
+                // look for next filename in load statement
               newFileLoc.append(state.substring(cp,
                       ncp = (state.indexOf("\"", ncp + 1) + 1)));
               String oldfilenam = state.substring(ncp,
@@ -2738,7 +2739,7 @@ public class Jalview2XML
               // have to normalize filename - since Jmol and jalview do filename
               // translation differently.
               Object[] filedat = oldFiles.get(new File(oldfilenam));
-              newFileLoc.append(((String) filedat[0]));
+              newFileLoc.append(Platform.escapeString((String) filedat[0]));
               pdbfilenames.addElement((String) filedat[0]);
               pdbids.addElement((String) filedat[1]);
               seqmaps.addElement((SequenceI[]) ((Vector<SequenceI>) filedat[2])
@@ -2746,6 +2747,7 @@ public class Jalview2XML
               newFileLoc.append("\"");
               cp = ecp + 1; // advance beyond last \" and set cursor so we can
                             // look for next file statement.
+              } while ((ncp=state.indexOf("/*file*/",cp))>-1);
             }
             if (cp > 0)
             {
@@ -2908,7 +2910,7 @@ public class Jalview2XML
 
     for (int i = 0; i < JSEQ.length; i++)
     {
-      af.viewport.setSequenceColour(af.viewport.alignment.getSequenceAt(i),
+      af.viewport.setSequenceColour(af.viewport.getAlignment().getSequenceAt(i),
               new java.awt.Color(JSEQ[i].getColour()));
     }
 
@@ -2919,7 +2921,7 @@ public class Jalview2XML
       jalview.gui.AlignViewport av = (jalview.gui.AlignViewport) viewportsAdded
               .get(uniqueSeqSetId);
 
-      af.viewport.sequenceSetID = uniqueSeqSetId;
+      af.viewport.setSequenceSetId(uniqueSeqSetId);
       if (av != null)
       {
         // propagate shared settings to this new view
@@ -3009,18 +3011,18 @@ public class Jalview2XML
       else if (view.getBgColour().startsWith("Annotation"))
       {
         // int find annotation
-        if (af.viewport.alignment.getAlignmentAnnotation() != null)
+        if (af.viewport.getAlignment().getAlignmentAnnotation() != null)
         {
-          for (int i = 0; i < af.viewport.alignment
+          for (int i = 0; i < af.viewport.getAlignment()
                   .getAlignmentAnnotation().length; i++)
           {
-            if (af.viewport.alignment.getAlignmentAnnotation()[i].label
+            if (af.viewport.getAlignment().getAlignmentAnnotation()[i].label
                     .equals(view.getAnnotationColours().getAnnotation()))
             {
-              if (af.viewport.alignment.getAlignmentAnnotation()[i]
+              if (af.viewport.getAlignment().getAlignmentAnnotation()[i]
                       .getThreshold() == null)
               {
-                af.viewport.alignment.getAlignmentAnnotation()[i]
+                af.viewport.getAlignment().getAlignmentAnnotation()[i]
                         .setThreshold(new jalview.datamodel.GraphLine(view
                                 .getAnnotationColours().getThreshold(),
                                 "Threshold", java.awt.Color.black)
@@ -3032,7 +3034,7 @@ public class Jalview2XML
                       .equals("None"))
               {
                 cs = new AnnotationColourGradient(
-                        af.viewport.alignment.getAlignmentAnnotation()[i],
+                        af.viewport.getAlignment().getAlignmentAnnotation()[i],
                         new java.awt.Color(view.getAnnotationColours()
                                 .getMinColour()), new java.awt.Color(view
                                 .getAnnotationColours().getMaxColour()),
@@ -3042,7 +3044,7 @@ public class Jalview2XML
                       .startsWith("ucs"))
               {
                 cs = new AnnotationColourGradient(
-                        af.viewport.alignment.getAlignmentAnnotation()[i],
+                        af.viewport.getAlignment().getAlignmentAnnotation()[i],
                         GetUserColourScheme(jms, view
                                 .getAnnotationColours().getColourScheme()),
                         view.getAnnotationColours().getAboveThreshold());
@@ -3050,7 +3052,7 @@ public class Jalview2XML
               else
               {
                 cs = new AnnotationColourGradient(
-                        af.viewport.alignment.getAlignmentAnnotation()[i],
+                        af.viewport.getAlignment().getAlignmentAnnotation()[i],
                         ColourSchemeProperty.getColour(al, view
                                 .getAnnotationColours().getColourScheme()),
                         view.getAnnotationColours().getAboveThreshold());
@@ -3073,7 +3075,7 @@ public class Jalview2XML
                    * if
                    * (view.getAnnotationColours().getColourScheme().equals("None"
                    * )) { sg.cs = new AnnotationColourGradient(
-                   * af.viewport.alignment.getAlignmentAnnotation()[i], new
+                   * af.viewport.getAlignment().getAlignmentAnnotation()[i], new
                    * java.awt.Color(view.getAnnotationColours().
                    * getMinColour()), new
                    * java.awt.Color(view.getAnnotationColours().
@@ -3082,7 +3084,7 @@ public class Jalview2XML
                    */
                   {
                     sg.cs = new AnnotationColourGradient(
-                            af.viewport.alignment.getAlignmentAnnotation()[i],
+                            af.viewport.getAlignment().getAlignmentAnnotation()[i],
                             sg.cs, view.getAnnotationColours()
                                     .getAboveThreshold());
                   }
@@ -3104,7 +3106,7 @@ public class Jalview2XML
       if (cs != null)
       {
         cs.setThreshold(view.getPidThreshold(), true);
-        cs.setConsensus(af.viewport.hconsensus);
+        cs.setConsensus(af.viewport.getSequenceConsensusHash());
       }
     }
 
@@ -3130,8 +3132,8 @@ public class Jalview2XML
     }
     if (view.hasIgnoreGapsinConsensus())
     {
-      af.viewport.ignoreGapsInConsensusCalculation = view
-              .getIgnoreGapsinConsensus();
+      af.viewport.setIgnoreGapsConsensus(view
+              .getIgnoreGapsinConsensus(), null);
     }
     if (view.hasFollowHighlight())
     {
@@ -3152,11 +3154,11 @@ public class Jalview2XML
     }
     if (view.hasShowSequenceLogo())
     {
-      af.viewport.showSequenceLogo = view.getShowSequenceLogo();
+      af.viewport.setShowSequenceLogo(view.getShowSequenceLogo());
     }
     else
     {
-      af.viewport.showSequenceLogo = false;
+      af.viewport.setShowSequenceLogo(false);
     }
     if (view.hasShowDbRefTooltip())
     {
@@ -3720,11 +3722,11 @@ public class Jalview2XML
     af.closeMenuItem_actionPerformed(true);
 
     /*
-     * if(ap.av.alignment.getAlignmentAnnotation()!=null) { for(int i=0;
-     * i<ap.av.alignment.getAlignmentAnnotation().length; i++) {
-     * if(!ap.av.alignment.getAlignmentAnnotation()[i].autoCalculated) {
-     * af.alignPanel.av.alignment.getAlignmentAnnotation()[i] =
-     * ap.av.alignment.getAlignmentAnnotation()[i]; } } }
+     * if(ap.av.getAlignment().getAlignmentAnnotation()!=null) { for(int i=0;
+     * i<ap.av.getAlignment().getAlignmentAnnotation().length; i++) {
+     * if(!ap.av.getAlignment().getAlignmentAnnotation()[i].autoCalculated) {
+     * af.alignPanel.av.getAlignment().getAlignmentAnnotation()[i] =
+     * ap.av.getAlignment().getAlignmentAnnotation()[i]; } } }
      */
 
     return af.alignPanel;