refactored from PopupMenu (for JAL-860)

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

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
old mode 100755 (executable)
new mode 100644 (file)
index 033b3bc..26fb890
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -40,6 +40,7 @@ import java.util.*;
 import java.awt.*;
 
 import jalview.analysis.*;
+import jalview.api.StructureSelectionManagerProvider;
 
 import jalview.bin.*;
 
@@ -48,14 +49,15 @@ import jalview.datamodel.*;
 import jalview.schemes.*;
 import jalview.structure.SelectionSource;
 import jalview.structure.StructureSelectionManager;
+import jalview.structure.VamsasSource;
 
 /**
  * DOCUMENT ME!
  * 
  * @author $author$
- * @version $Revision$
+ * @version $Revision: 1.141 $
  */
-public class AlignViewport implements SelectionSource
+public class AlignViewport implements SelectionSource, VamsasSource
 {
   private static final int RIGHT_JUSTIFY = 1;
 
@@ -642,9 +644,9 @@ public class AlignViewport implements SelectionSource
   }
 
   /**
-   * DOCUMENT ME!
    * 
-   * @return DOCUMENT ME!
+   * 
+   * @return null or the currently selected sequence region
    */
   public SequenceGroup getSelectionGroup()
   {
@@ -652,10 +654,10 @@ public class AlignViewport implements SelectionSource
   }
 
   /**
-   * DOCUMENT ME!
+   * Set the selection group for this window.
    * 
-   * @param sg
-   *          DOCUMENT ME!
+   * @param sg - group holding references to sequences in this alignment view
+   *          
    */
   public void setSelectionGroup(SequenceGroup sg)
   {
@@ -663,9 +665,8 @@ public class AlignViewport implements SelectionSource
   }
 
   /**
-   * DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
+   * GUI state
+   * @return true if conservation based shading is enabled
    */
   public boolean getConservationSelected()
   {
@@ -673,10 +674,9 @@ public class AlignViewport implements SelectionSource
   }
 
   /**
-   * DOCUMENT ME!
-   * 
+   * GUI state
    * @param b
-   *          DOCUMENT ME!
+   *          enable conservation based shading
    */
   public void setConservationSelected(boolean b)
   {
@@ -684,9 +684,8 @@ public class AlignViewport implements SelectionSource
   }
 
   /**
-   * DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
+   * GUI state
+   * @return true if percent identity threshold is applied to shading
    */
   public boolean getAbovePIDThreshold()
   {
@@ -694,10 +693,10 @@ public class AlignViewport implements SelectionSource
   }
 
   /**
-   * DOCUMENT ME!
+   * GUI state
    * 
-   * @param b
-   *          DOCUMENT ME!
+   * 
+   * @param b indicate if percent identity threshold is applied to shading
    */
   public void setAbovePIDThreshold(boolean b)
   {
@@ -942,13 +941,13 @@ public class AlignViewport implements SelectionSource
   {
     if (alignment != null && alignment.getCodonFrames() != null)
     {
-      StructureSelectionManager.getStructureSelectionManager()
+      StructureSelectionManager.getStructureSelectionManager(Desktop.instance)
               .removeMappings(alignment.getCodonFrames());
     }
     this.alignment = align;
     if (alignment.getCodonFrames() != null)
     {
-      StructureSelectionManager.getStructureSelectionManager().addMappings(
+      StructureSelectionManager.getStructureSelectionManager(Desktop.instance).addMappings(
               alignment.getCodonFrames());
     }
   }
@@ -2016,32 +2015,34 @@ public class AlignViewport implements SelectionSource
   /**
    * checks current SelectionGroup against record of last hash value, and
    * updates record.
+   * @param b update the record of last hash value
    * 
-   * @return true if SelectionGroup changed since last call
+   * @return true if SelectionGroup changed since last call (when b is true)
    */
-  boolean isSelectionGroupChanged()
+  boolean isSelectionGroupChanged(boolean b)
   {
-    int hc = (selectionGroup == null) ? -1 : selectionGroup.hashCode();
-    if (hc != sgrouphash)
+    int hc = (selectionGroup == null || selectionGroup.getSize()==0) ? -1 : selectionGroup.hashCode();
+    if (hc!=-1 && hc != sgrouphash)
     {
-      sgrouphash = hc;
+      if (b) {sgrouphash = hc;}
       return true;
     }
     return false;
   }
 
   /**
-   * checks current colsel against record of last hash value, and updates
+   * checks current colsel against record of last hash value, and optionally updates
    * record.
-   * 
-   * @return true if colsel changed since last call
+
+   * @param b update the record of last hash value
+   * @return true if colsel changed since last call (when b is true)
    */
-  boolean isColSelChanged()
+  boolean isColSelChanged(boolean b)
   {
-    int hc = (colSel == null) ? -1 : colSel.hashCode();
-    if (hc != colselhash)
+    int hc = (colSel == null || colSel.size()==0) ? -1 : colSel.hashCode();
+    if (hc!=-1 && hc != colselhash)
     {
-      colselhash = hc;
+      if (b) {colselhash = hc;}
       return true;
     }
     return false;
@@ -2050,7 +2051,7 @@ public class AlignViewport implements SelectionSource
   public void sendSelection()
   {
     jalview.structure.StructureSelectionManager
-            .getStructureSelectionManager().sendSelection(
+            .getStructureSelectionManager(Desktop.instance).sendSelection(
                     new SequenceGroup(getSelectionGroup()),
                     new ColumnSelection(getColumnSelection()), this);
   }
@@ -2242,4 +2243,43 @@ public class AlignViewport implements SelectionSource
       }
     }
   }
+
+  public StructureSelectionManager getStructureSelectionManager()
+  {
+    return StructureSelectionManager.getStructureSelectionManager(Desktop.instance);
+  }
+
+  /**
+   * 
+   * @param pdbEntries
+   * @return a series of SequenceI arrays, one for each PDBEntry, listing which sequence in the alignment holds a reference to it
+   */
+  public SequenceI[][] collateForPDB(PDBEntry[] pdbEntries)
+  {
+    ArrayList<SequenceI[]> seqvectors = new ArrayList<SequenceI[]>();
+    for (PDBEntry pdb: pdbEntries) {
+    ArrayList<SequenceI> seqs = new ArrayList<SequenceI>();
+    for (int i = 0; i < alignment.getHeight(); i++)
+    {
+      Vector pdbs = alignment.getSequenceAt(i)
+              .getDatasetSequence().getPDBId();
+      if (pdbs == null)
+        continue;
+      SequenceI sq;
+      for (int p = 0; p < pdbs.size(); p++)
+      {
+        PDBEntry p1 = (PDBEntry) pdbs.elementAt(p);
+        if (p1.getId().equals(pdb.getId()))
+        {
+          if (!seqs.contains(sq=alignment.getSequenceAt(i)))
+            seqs.add(sq);
+
+          continue;
+        }
+      }
+    }
+    seqvectors.add(seqs.toArray(new SequenceI[seqs.size()]));
+    }
+    return seqvectors.toArray(new SequenceI[seqvectors.size()][]);
+  }
 }