JAL-3210 Barebones gradle/buildship/eclipse. See README

[jalview.git] / src / jalview / controller / AlignViewController.java

diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java
index cc5a184..9b8a9e3 100644 (file)
--- a/src/jalview/controller/AlignViewController.java
+++ b/src/jalview/controller/AlignViewController.java
@@ -35,8 +35,8 @@ import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.io.DataSourceType;
 import jalview.io.FeaturesFile;
+import jalview.schemes.ColourSchemeI;
 import jalview.util.MessageManager;
-import jalview.viewmodel.seqfeatures.FeatureRendererModel;
 
 import java.awt.Color;
 import java.util.BitSet;
@@ -54,20 +54,19 @@ public class AlignViewController implements AlignViewControllerI
   private AlignViewControllerGuiI avcg;
 
   public AlignViewController(AlignViewControllerGuiI alignFrame,
-          AlignViewportI viewport, AlignmentViewPanel alignPanel)
+          AlignViewportI vp, AlignmentViewPanel ap)
   {
     this.avcg = alignFrame;
-    this.viewport = viewport;
-    this.alignPanel = alignPanel;
+    this.viewport = vp;
+    this.alignPanel = ap;
   }
 
   @Override
-  public void setViewportAndAlignmentPanel(AlignViewportI viewport,
-          AlignmentViewPanel alignPanel)
+  public void setViewportAndAlignmentPanel(AlignViewportI vp,
+          AlignmentViewPanel ap)
   {
-    this.alignPanel = alignPanel;
-    this.viewport = viewport;
-
+    this.alignPanel = ap;
+    this.viewport = vp;
   }
 
   @Override
@@ -99,19 +98,22 @@ public class AlignViewController implements AlignViewControllerI
       viewport.getAlignment().deleteAllGroups();
       viewport.clearSequenceColours();
       viewport.setSelectionGroup(null);
+      ColourSchemeI colours = viewport.getGlobalColourScheme();
       // set view properties for each group
       for (int g = 0; g < gps.length; g++)
       {
         // gps[g].setShowunconserved(viewport.getShowUnconserved());
         gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
         viewport.getAlignment().addGroup(gps[g]);
-        Color col = new Color((int) (Math.random() * 255),
-                (int) (Math.random() * 255), (int) (Math.random() * 255));
-        col = col.brighter();
-        for (SequenceI sq : gps[g].getSequences(null))
+        if (colours != null)
         {
-          viewport.setSequenceColour(sq, col);
+          gps[g].setColourScheme(colours.getInstance(viewport, gps[g]));
         }
+        Color col = new Color((int) (Math.random() * 255),
+                (int) (Math.random() * 255), (int) (Math.random() * 255));
+        gps[g].idColour = col;
+        viewport.setUpdateStructures(true);
+        viewport.addSequenceGroup(gps[g]);
       }
       return true;
     }
@@ -164,9 +166,10 @@ public class AlignViewController implements AlignViewControllerI
     // JBPNote this routine could also mark rows, not just columns.
     // need a decent query structure to allow all types of feature searches
     BitSet bs = new BitSet();
-    SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null
-            || extendCurrent) ? viewport.getAlignment()
-                    : viewport.getSelectionGroup();
+    boolean searchSelection = viewport.getSelectionGroup() != null
+            && !extendCurrent;
+    SequenceCollectionI sqcol = searchSelection ? viewport
+            .getSelectionGroup() : viewport.getAlignment();
 
     int nseq = findColumnsWithFeature(featureType, sqcol, bs);
 
@@ -202,9 +205,10 @@ public class AlignViewController implements AlignViewControllerI
     }
     else
     {
-      avcg.setStatus(MessageManager
-              .formatMessage("label.no_feature_of_type_found", new String[]
-              { featureType }));
+      String key = searchSelection ? "label.no_feature_found_selection"
+              : "label.no_feature_of_type_found";
+      avcg.setStatus(MessageManager.formatMessage(key,
+              new String[] { featureType }));
       if (!extendCurrent)
       {
         cs.clear();
@@ -216,8 +220,9 @@ public class AlignViewController implements AlignViewControllerI
 
   /**
    * Sets a bit in the BitSet for each column (base 0) in the sequence
-   * collection which includes the specified feature type. Returns the number of
-   * sequences which have the feature in the selected range.
+   * collection which includes a visible feature of the specified feature type.
+   * Returns the number of sequences which have the feature visible in the
+   * selected range.
    * 
    * @param featureType
    * @param sqcol
@@ -227,9 +232,8 @@ public class AlignViewController implements AlignViewControllerI
   int findColumnsWithFeature(String featureType,
           SequenceCollectionI sqcol, BitSet bs)
   {
-    FeatureRendererModel fr = (FeatureRendererModel) alignPanel
+    FeatureRenderer fr = alignPanel == null ? null : alignPanel
             .getFeatureRenderer();
-    List<String> visibleFeatures = fr.getDisplayedFeatureTypes();
 
     final int startColumn = sqcol.getStartRes() + 1; // converted to base 1
     final int endColumn = sqcol.getEndRes() + 1;
@@ -243,20 +247,19 @@ public class AlignViewController implements AlignViewControllerI
         List<SequenceFeature> sfs = sq.findFeatures(startColumn,
                 endColumn, featureType);
 
-        if (!sfs.isEmpty())
-        {
-          nseq++;
-        }
-
+        boolean found = false;
         for (SequenceFeature sf : sfs)
         {
-          { 
-            if (!visibleFeatures.contains(sf.getType()) 
-                    || fr.getColour(sf) == null) // could pull up getColour to FeatureRenderer interface 
-            { 
-              continue; 
-            }
+          if (fr.getColour(sf) == null)
+          {
+            continue;
           }
+          if (!found)
+          {
+            nseq++;
+          }
+          found = true;
+
           int sfStartCol = sq.findIndex(sf.getBegin());
           int sfEndCol = sq.findIndex(sf.getEnd());
 
@@ -352,28 +355,28 @@ public class AlignViewController implements AlignViewControllerI
   }
 
   @Override
-  public boolean parseFeaturesFile(String file, DataSourceType protocol,
+  public boolean parseFeaturesFile(Object file, DataSourceType protocol,
           boolean relaxedIdMatching)
   {
-    boolean featuresFile = false;
+    boolean featuresAdded = false;
+    FeatureRenderer fr = alignPanel.getFeatureRenderer();
     try
     {
-      featuresFile = new FeaturesFile(false, file, protocol).parse(
-              viewport.getAlignment().getDataset(),
-              alignPanel.getFeatureRenderer().getFeatureColours(), false,
-              relaxedIdMatching);
+      featuresAdded = new FeaturesFile(false, file, protocol).parse(
+              viewport.getAlignment().getDataset(), fr.getFeatureColours(),
+              fr.getFeatureFilters(), false, relaxedIdMatching);
     } catch (Exception ex)
     {
       ex.printStackTrace();
     }
 
-    if (featuresFile)
+    if (featuresAdded)
     {
       avcg.refreshFeatureUI(true);
-      if (alignPanel.getFeatureRenderer() != null)
+      if (fr != null)
       {
         // update the min/max ranges where necessary
-        alignPanel.getFeatureRenderer().findAllFeatures(true);
+        fr.findAllFeatures(true);
       }
       if (avcg.getFeatureSettingsUI() != null)
       {
@@ -382,7 +385,7 @@ public class AlignViewController implements AlignViewControllerI
       alignPanel.paintAlignment(true, true);
     }
 
-    return featuresFile;
+    return featuresAdded;
 
   }