(JAL-969) refactored alignmentViewport base class to own package and pulled up most...

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

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index d5b5fae..dc1ef4f 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -426,9 +426,9 @@ 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 +497,13 @@ 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++)
           {
@@ -706,9 +704,9 @@ 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)
@@ -764,7 +762,7 @@ 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());
@@ -864,8 +862,8 @@ 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);
@@ -1204,7 +1202,7 @@ public class Jalview2XML
 
     }
 
-    if (av.hasHiddenColumns)
+    if (av.hasHiddenColumns())
     {
       if (av.getColumnSelection() == null
               || av.getColumnSelection().getHiddenColumns() == null)
@@ -2907,7 +2905,7 @@ 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()));
     }
 
@@ -2918,7 +2916,7 @@ 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
@@ -3008,18 +3006,18 @@ 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)
@@ -3031,7 +3029,7 @@ 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()),
@@ -3041,7 +3039,7 @@ 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());
@@ -3049,7 +3047,7 @@ 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());
@@ -3072,7 +3070,7 @@ 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().
@@ -3081,7 +3079,7 @@ public class Jalview2XML
                    */
                   {
                     sg.cs = new AnnotationColourGradient(
-                            af.viewport.alignment.getAlignmentAnnotation()[i],
+                            af.viewport.getAlignment().getAlignmentAnnotation()[i],
                             sg.cs, view.getAnnotationColours()
                                     .getAboveThreshold());
                   }
@@ -3103,7 +3101,7 @@ public class Jalview2XML
       if (cs != null)
       {
         cs.setThreshold(view.getPidThreshold(), true);
-        cs.setConsensus(af.viewport.hconsensus);
+        cs.setConsensus(af.viewport.getSequenceConsensusHash());
       }
     }
 
@@ -3129,8 +3127,8 @@ public class Jalview2XML
     }
     if (view.hasIgnoreGapsinConsensus())
     {
-      af.viewport.ignoreGapsInConsensusCalculation = view
-              .getIgnoreGapsinConsensus();
+      af.viewport.setIgnoreGapsConsensus(view
+              .getIgnoreGapsinConsensus(), null);
     }
     if (view.hasFollowHighlight())
     {
@@ -3151,11 +3149,11 @@ 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())
     {
@@ -3719,11 +3717,11 @@ 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;