Functions for parsing free text properties on sequences, alignments and annotations.

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

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 3c8d31a..f0551e8 100755 (executable)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -51,6 +51,10 @@ public class Jalview2XML
   Hashtable annotationIds = new Hashtable();
 
   String uniqueSetSuffix = "";
+  /**
+   * List of pdbfiles added to Jar
+   */
+  Vector pdbfiles = null;
 
   // SAVES SEVERAL ALIGNMENT WINDOWS TO SAME JARFILE
   public void SaveState(File statefile)
@@ -206,7 +210,6 @@ public class Jalview2XML
     vamsasSet.setGapChar(jal.getGapCharacter() + "");
 
     JSeq jseq;
-    Vector pdbfiles = null;
 
     //SAVE SEQUENCES
     int id = 0;
@@ -527,32 +530,40 @@ public class Jalview2XML
         }
 
         an.setLabel(aa[i].label);
-
+        if (aa[i].hasScore())
+        {
+          an.setScore(aa[i].getScore());
+        }
         AnnotationElement ae;
-
-        for (int a = 0; a < aa[i].annotations.length; a++)
+        if (aa[i].annotations!=null)
         {
-          if ( (aa[i] == null) || (aa[i].annotations[a] == null))
+          an.setScoreOnly(false);
+          for (int a = 0; a < aa[i].annotations.length; a++)
           {
-            continue;
-          }
+            if ((aa[i] == null) || (aa[i].annotations[a] == null))
+            {
+              continue;
+            }
 
-          ae = new AnnotationElement();
-          ae.setDescription(aa[i].annotations[a].description);
-          ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
-          ae.setValue(aa[i].annotations[a].value);
-          ae.setPosition(a);
-          ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure +
-                                   "");
+            ae = new AnnotationElement();
+            ae.setDescription(aa[i].annotations[a].description);
+            ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
+            ae.setValue(aa[i].annotations[a].value);
+            ae.setPosition(a);
+            ae
+                    .setSecondaryStructure(aa[i].annotations[a].secondaryStructure
+                            + "");
 
-          if (aa[i].annotations[a].colour != java.awt.Color.black)
-          {
-            ae.setColour(aa[i].annotations[a].colour.getRGB());
-          }
+            if (aa[i].annotations[a].colour != java.awt.Color.black)
+            {
+              ae.setColour(aa[i].annotations[a].colour.getRGB());
+            }
 
-          an.addAnnotationElement(ae);
+            an.addAnnotationElement(ae);
+          }
+        } else {
+          an.setScoreOnly(true);
         }
-
         vamsasSet.addAnnotation(an);
       }
     }
@@ -751,11 +762,14 @@ public class Jalview2XML
         setting.setDisplay(
             av.featuresDisplayed.containsKey(renderOrder[ro])
             );
-
+        float rorder=ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder(renderOrder[ro]);
+        if (rorder>-1) {
+          setting.setOrder(rorder);
+        }
         fs.addSetting(setting);
         settingsAdded.addElement(renderOrder[ro]);
       }
-
+      
       //Make sure we save none displayed feature settings
       Enumeration en =
           ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours.keys();
@@ -774,11 +788,29 @@ public class Jalview2XML
             );
 
         setting.setDisplay(false);
-
+        float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder(key);
+        if (rorder>-1) 
+        {
+          setting.setOrder(rorder);
+        }
         fs.addSetting(setting);
         settingsAdded.addElement(key);
       }
-
+      en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups.keys();
+      Vector groupsAdded=new Vector(); 
+      while (en.hasMoreElements())
+      {
+        String grp = en.nextElement().toString();
+        if (groupsAdded.contains(grp)) 
+        {
+          continue;
+        }
+        Group g = new Group();
+        g.setName(grp);
+        g.setDisplay(((Boolean)ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups.get(grp)).booleanValue());
+        fs.addGroup(g);
+        groupsAdded.addElement(grp);
+      }
       jms.setFeatureSettings(fs);
 
     }
@@ -1286,21 +1318,24 @@ public class Jalview2XML
         }
 
         AnnotationElement[] ae = an[i].getAnnotationElement();
-        jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[
-            al.getWidth()];
+        jalview.datamodel.Annotation[] anot = null;
+        if (!an[i].getScoreOnly())
+        { 
+          anot = new jalview.datamodel.Annotation[
+                    al.getWidth()];
 
-        for (int aa = 0; aa < ae.length && aa < anot.length; aa++)
-        {
-          anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].
-              getDisplayCharacter(),
-              ae[aa].getDescription(),
-              ae[aa].getSecondaryStructure().length() == 0 ? ' ' :
-              ae[aa].getSecondaryStructure().charAt(0),
-                   ae[aa].getValue());
-          anot[ae[aa].getPosition()].colour = new java.awt.Color(ae[aa].
-              getColour());
+          for (int aa = 0; aa < ae.length && aa < anot.length; aa++)
+          {
+            anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].
+                    getDisplayCharacter(),
+                    ae[aa].getDescription(),
+                    ae[aa].getSecondaryStructure().length() == 0 ? ' ' :
+                      ae[aa].getSecondaryStructure().charAt(0),
+                      ae[aa].getValue());
+            anot[ae[aa].getPosition()].colour = new java.awt.Color(ae[aa].
+                    getColour());
+          }
         }
-
         jalview.datamodel.AlignmentAnnotation jaa = null;
 
         if (an[i].getGraph())
@@ -1341,7 +1376,10 @@ public class Jalview2XML
               );
           al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
         }
-
+        if (an[i].hasScore())
+        {
+          jaa.setScore(an[i].getScore());
+        }
         al.addAnnotation(jaa);
       }
     }
@@ -1698,9 +1736,11 @@ public class Jalview2XML
         af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(setting.
             getType(),
             new java.awt.Color(setting.getColour()));
-
         renderOrder[fs] = setting.getType();
-
+        if (setting.hasOrder())
+          af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(setting.getType(), setting.getOrder());
+        else
+          af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(setting.getType(), fs/jms.getFeatureSettings().getSettingCount());
         if (setting.getDisplay())
         {
           af.viewport.featuresDisplayed.put(
@@ -1709,8 +1749,15 @@ public class Jalview2XML
       }
       af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder =
           renderOrder;
+      Hashtable fgtable;
+      af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureGroups = fgtable=new Hashtable();
+      for (int gs=0;gs<jms.getFeatureSettings().getGroupCount(); gs++) 
+      {
+        Group grp = jms.getFeatureSettings().getGroup(gs);
+        fgtable.put(grp.getName(), new Boolean(grp.getDisplay()));
+      }
     }
-
+    
     if (view.getHiddenColumnsCount() > 0)
     {
       for (int c = 0; c < view.getHiddenColumnsCount(); c++)
@@ -1828,10 +1875,13 @@ public class Jalview2XML
                             new java.awt.Rectangle(x, y, width, height));
 
               }
-              else
+              else if(comp!=null)
               {
                 StructureSelectionManager.getStructureSelectionManager()
-                    .setMapping(seq, pdbFile, jalview.io.AppletFormatAdapter.FILE);
+                    .setMapping(seq, pdbFile,
+                                jalview.io.AppletFormatAdapter.FILE);
+
+                ( (AppJMol) comp).addSequence(seq);
               }
             }
           }