From 410dfa093c4150aeadc02710c2a70eb862e3b2d8 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 25 Jan 2007 18:46:31 +0000
Subject: [PATCH] Annotations move when full alignment edited

---
 src/jalview/appletgui/AlignFrame.java |    4 ++--
 src/jalview/appletgui/SeqPanel.java   |   16 ++++++-------
 src/jalview/gui/AlignFrame.java       |    8 +++----
 src/jalview/gui/Jalview2XML.java      |   40 ++++++++++++++++++++++++++++++++-
 src/jalview/gui/SeqPanel.java         |   16 ++++++-------
 5 files changed, 61 insertions(+), 23 deletions(-)

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 4115999..36ee5da 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -1360,7 +1360,7 @@ public void itemStateChanged(ItemEvent evt)
         new RemoveGapColCommand("Remove Gapped Columns",
                                 seqs,
                                 start, end,
-                                viewport.getGapCharacter());
+                                viewport.alignment);
 
     addHistoryItem(removeGapCols);
 
@@ -1402,7 +1402,7 @@ public void itemStateChanged(ItemEvent evt)
     addHistoryItem(new RemoveGapsCommand("Remove Gaps",
                                            seqs,
                                            start, end,
-                     viewport.getGapCharacter()));
+                     viewport.alignment));
 
     viewport.setStartRes(seq.findIndex(startRes)-1);
 
diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index 89e2086..6b93206 100755
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -956,7 +956,7 @@ public class SeqPanel
               editCommand.appendEdit(EditCommand.INSERT_GAP,
                                      groupSeqs,
                                      startres, startres-lastres,
-                                     av.getGapCharacter(),
+                                     av.alignment,
                                      true);
             }
           }
@@ -974,7 +974,7 @@ public class SeqPanel
               editCommand.appendEdit(EditCommand.DELETE_GAP,
                                      groupSeqs,
                                      startres, lastres - startres,
-                                     av.getGapCharacter(),
+                                     av.alignment,
                                      true);
 
           }
@@ -997,7 +997,7 @@ public class SeqPanel
                                    new SequenceI[]
                                    {seq},
                                    lastres, startres-lastres,
-                                   av.getGapCharacter(),
+                                   av.alignment,
                                    true);
           }
         }
@@ -1033,7 +1033,7 @@ public class SeqPanel
                                      new SequenceI[]
                                      {seq},
                                      startres, max,
-                                     av.getGapCharacter(),
+                                     av.alignment,
                                      true);
             }
           }
@@ -1073,11 +1073,11 @@ public class SeqPanel
 
     editCommand.appendEdit(EditCommand.DELETE_GAP,
                            seq,
-                           blankColumn, 1, av.getGapCharacter(), true);
+                           blankColumn, 1, av.alignment, true);
 
     editCommand.appendEdit(EditCommand.INSERT_GAP,
                            seq,
-                           j, 1, av.getGapCharacter(),
+                           j, 1, av.alignment,
                            true);
 
   }
@@ -1087,11 +1087,11 @@ public class SeqPanel
 
     editCommand.appendEdit(EditCommand.DELETE_GAP,
                            seq,
-                           j, 1, av.getGapCharacter(), true);
+                           j, 1, av.alignment, true);
 
     editCommand.appendEdit(EditCommand.INSERT_GAP,
                            seq,
-                           fixedColumn, 1, av.getGapCharacter(), true);
+                           fixedColumn, 1, av.alignment, true);
   }
 
 
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index b2fa937..7b1dfeb 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1691,7 +1691,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
         new RemoveGapColCommand("Remove Gapped Columns",
                                 seqs,
                                 start, end,
-                                viewport.getGapCharacter());
+                                viewport.alignment);
 
     addHistoryItem(removeGapCols);
 
@@ -1736,9 +1736,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     int startRes = seq.findPosition(viewport.startRes);
 
     addHistoryItem(new RemoveGapsCommand("Remove Gaps",
-                                           seqs,
-                                           start, end,
-                     viewport.getGapCharacter()));
+                                         seqs,
+                                         start, end,
+                                         viewport.alignment));
 
     viewport.setStartRes(seq.findIndex(startRes)-1);
 
diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 6652aea..0cac9c1 100755
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -56,6 +56,8 @@ public class Jalview2XML
    */
   Hashtable viewportsAdded;
 
+  Hashtable annotationIds = new Hashtable();
+
   String uniqueSetSuffix = "";
 
 
@@ -454,6 +456,13 @@ public class Jalview2XML
             {
                 Annotation an = new Annotation();
 
+                if(aa[i].annotationId!=null)
+                {
+                  annotationIds.put(aa[i].annotationId, aa[i]);
+                }
+
+                an.setId(aa[i].annotationId);
+
                 if (aa[i].label.equals("Quality") ||
                         aa[i].label.equals("Conservation") ||
                         aa[i].label.equals("Consensus"))
@@ -957,6 +966,7 @@ public class Jalview2XML
             System.out.println("Successfully loaded archive file");
             return af;
           }
+          ex.printStackTrace();
 
             System.err.println("Exception whilst loading jalview XML file : " +
                 ex + "\n");
@@ -1205,10 +1215,20 @@ public class Jalview2XML
                  continue;
                }
 
+               if (an[i].getId() != null
+                   && annotationIds.containsKey(an[i].getId()))
+               {
+                 al.addAnnotation(
+                     (jalview.datamodel.AlignmentAnnotation)annotationIds.get(an[i].getId())
+                     );
+
+                 continue;
+              }
+
                 AnnotationElement[] ae = an[i].getAnnotationElement();
                 jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al.getWidth()];
 
-                for (int aa = 0; aa < ae.length; aa++)
+                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(),
@@ -1244,6 +1264,12 @@ public class Jalview2XML
                             an[i].getDescription(), anot);
                 }
 
+                if(an[i].getId()!=null)
+                {
+                  annotationIds.put(an[i].getId(), jaa);
+                  jaa.annotationId = an[i].getId();
+                }
+
                 if(an[i].getSequenceRef()!=null)
                 {
                   jaa.createSequenceMapping(
@@ -1685,6 +1711,18 @@ public class Jalview2XML
       af.alignPanels.clear();
       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];
+          }
+        }
+      }   */
+
       return af.alignPanel;
     }
 }
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 675325a..8de1d01 100755
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -1037,7 +1037,7 @@ public class SeqPanel extends JPanel implements MouseListener,
                 editCommand.appendEdit(EditCommand.INSERT_GAP,
                                        groupSeqs,
                                        startres, startres-lastres,
-                                       av.getGapCharacter(),
+                                       av.alignment,
                                        true);
               }
             }
@@ -1055,7 +1055,7 @@ public class SeqPanel extends JPanel implements MouseListener,
                 editCommand.appendEdit(EditCommand.DELETE_GAP,
                                        groupSeqs,
                                        startres, lastres - startres,
-                                       av.getGapCharacter(),
+                                       av.alignment,
                                        true);
 
             }
@@ -1078,7 +1078,7 @@ public class SeqPanel extends JPanel implements MouseListener,
                                      new SequenceI[]
                                      {seq},
                                      lastres, startres-lastres,
-                                     av.getGapCharacter(),
+                                     av.alignment,
                                      true);
             }
           }
@@ -1114,7 +1114,7 @@ public class SeqPanel extends JPanel implements MouseListener,
                                        new SequenceI[]
                                        {seq},
                                        startres, max,
-                                       av.getGapCharacter(),
+                                       av.alignment,
                                        true);
               }
             }
@@ -1154,11 +1154,11 @@ public class SeqPanel extends JPanel implements MouseListener,
 
       editCommand.appendEdit(EditCommand.DELETE_GAP,
                              seq,
-                             blankColumn, 1, av.getGapCharacter(), true);
+                             blankColumn, 1, av.alignment, true);
 
       editCommand.appendEdit(EditCommand.INSERT_GAP,
                              seq,
-                             j, 1, av.getGapCharacter(),
+                             j, 1, av.alignment,
                              true);
 
     }
@@ -1168,11 +1168,11 @@ public class SeqPanel extends JPanel implements MouseListener,
 
       editCommand.appendEdit(EditCommand.DELETE_GAP,
                              seq,
-                             j, 1, av.getGapCharacter(), true);
+                             j, 1, av.alignment, true);
 
       editCommand.appendEdit(EditCommand.INSERT_GAP,
                              seq,
-                             fixedColumn, 1, av.getGapCharacter(), true);
+                             fixedColumn, 1, av.alignment, true);
     }
 
     /**
-- 
1.7.10.2