JAL-1115 refactor base collection for Alignment from Vector to locally synchronized...

[jalview.git] / src / jalview / appletgui / AlignFrame.java

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 834b904..9e5c4fb 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -35,6 +35,7 @@ import jalview.datamodel.AlignmentOrder;
 import jalview.datamodel.ColumnSelection;\r
 import jalview.datamodel.PDBEntry;\r
 import jalview.datamodel.Sequence;\r
+import jalview.datamodel.SequenceCollectionI;\r
 import jalview.datamodel.SequenceGroup;\r
 import jalview.datamodel.SequenceI;\r
 import jalview.io.AnnotationFile;\r
@@ -87,6 +88,7 @@ import java.net.URL;
 import java.net.URLEncoder;\r
 import java.util.Enumeration;\r
 import java.util.Hashtable;\r
+import java.util.List;\r
 import java.util.StringTokenizer;\r
 import java.util.Vector;\r
 \r
@@ -956,9 +958,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
     else if (source == clustalColour)\r
     {\r
       abovePIDThreshold.setState(false);\r
-      changeColour(new ClustalxColourScheme(\r
-              viewport.getAlignment().getSequences(),\r
-              viewport.getAlignment().getWidth()));\r
+      changeColour(new ClustalxColourScheme(viewport.getAlignment(),null));\r
     }\r
     else if (source == zappoColour)\r
     {\r
@@ -1504,10 +1504,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
 \r
   synchronized void slideSequences(boolean right, int size)\r
   {\r
-    Vector sg = new Vector();\r
+    List<SequenceI>sg = new Vector<SequenceI>();\r
     if (viewport.cursorMode)\r
     {\r
-      sg.addElement(viewport.getAlignment()\r
+      sg.add(viewport.getAlignment()\r
               .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));\r
     }\r
     else if (viewport.getSelectionGroup() != null\r
@@ -1523,7 +1523,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
       return;\r
     }\r
 \r
-    Vector invertGroup = new Vector();\r
+    Vector<SequenceI> invertGroup = new Vector();\r
 \r
     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)\r
     {\r
@@ -1531,11 +1531,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
         invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));\r
     }\r
 \r
-    SequenceI[] seqs1 = new SequenceI[sg.size()];\r
-    for (int i = 0; i < sg.size(); i++)\r
-      seqs1[i] = (SequenceI) sg.elementAt(i);\r
+    SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);\r
 \r
-    SequenceI[] seqs2 = new SequenceI[invertGroup.size()];\r
+    SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup.size()]);\r
     for (int i = 0; i < invertGroup.size(); i++)\r
       seqs2[i] = (SequenceI) invertGroup.elementAt(i);\r
 \r
@@ -1898,9 +1896,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
         Color col = new Color((int) (Math.random() * 255),\r
                 (int) (Math.random() * 255), (int) (Math.random() * 255));\r
         col = col.brighter();\r
-        for (Enumeration sq = gps[g].getSequences(null).elements(); sq\r
-                .hasMoreElements(); viewport.setSequenceColour(\r
-                (SequenceI) sq.nextElement(), col))\r
+        for (SequenceI sq : gps[g].getSequences(null))\r
+          viewport.setSequenceColour(\r
+                sq, col)\r
           ;\r
       }\r
       PaintRefresher.Refresh(this, viewport.getSequenceSetId());\r
@@ -2017,12 +2015,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
 \r
       addHistoryItem(trimRegion);\r
 \r
-      Vector groups = viewport.getAlignment().getGroups();\r
 \r
-      for (int i = 0; i < groups.size(); i++)\r
-      {\r
-        SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
 \r
+      for (SequenceGroup sg:viewport.getAlignment().getGroups())\r
+      {\r
         if ((trimLeft && !sg.adjustForRemoveLeft(column))\r
                 || (!trimLeft && !sg.adjustForRemoveRight(column)))\r
         {\r
@@ -2351,68 +2347,6 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
     }             \r
     viewport.setGlobalColourScheme(cs);\r
 \r
-    if (viewport.getColourAppliesToAllGroups())\r
-    {\r
-      Vector groups = viewport.getAlignment().getGroups();\r
-      for (int i = 0; i < groups.size(); i++)\r
-      {\r
-        SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
-\r
-        if (cs == null)\r
-        {\r
-          sg.cs = null;\r
-          continue;\r
-        }\r
-        if (cs instanceof ClustalxColourScheme)\r
-        {\r
-          sg.cs = new ClustalxColourScheme(\r
-                  sg.getSequences(viewport.getHiddenRepSequences()),\r
-                  sg.getWidth());\r
-        }\r
-        else\r
-        {\r
-          try\r
-          {\r
-            sg.cs = cs.getClass().newInstance();\r
-          } catch (Exception ex)\r
-          {\r
-            ex.printStackTrace();\r
-            sg.cs = cs;\r
-          }\r
-        }\r
-\r
-        if (viewport.getAbovePIDThreshold()\r
-                || cs instanceof PIDColourScheme\r
-                || cs instanceof Blosum62ColourScheme)\r
-        {\r
-          sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
-          sg.cs.setConsensus(AAFrequency.calculate(\r
-                  sg.getSequences(viewport.getHiddenRepSequences()), 0,\r
-                  sg.getWidth()));\r
-        }\r
-        else\r
-        {\r
-          sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
-        }\r
-\r
-        if (viewport.getConservationSelected())\r
-        {\r
-          Conservation c = new Conservation("Group",\r
-                  ResidueProperties.propHash, 3,\r
-                  sg.getSequences(viewport.getHiddenRepSequences()), 0,\r
-                  viewport.getAlignment().getWidth() - 1);\r
-          c.calculate();\r
-          c.verdict(false, viewport.getConsPercGaps());\r
-          sg.cs.setConservation(c);\r
-        }\r
-        else\r
-        {\r
-          sg.cs.setConservation(null);\r
-          sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
-        }\r
-\r
-      }\r
-    }\r
 \r
     if (alignPanel.getOverviewPanel() != null)\r
     {\r