Submissions for secondary structure prediction are now filtered to remove empty seque...

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 74f081b..81e5564 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -276,7 +276,6 @@ public class AlignFrame
       }\r
 \r
       viewport.showSequenceFeatures = true;\r
-      ((Alignment)viewport.alignment).featuresAdded = true;\r
 \r
       alignPanel.repaint();\r
 \r
@@ -736,7 +735,6 @@ public class AlignFrame
     }\r
 \r
     FastaFile ff = new FastaFile();\r
-    ff.addDBPrefix( viewport.showDBPrefix );\r
     ff.addJVSuffix( viewport.showJVSuffix );\r
     c.setContents(new StringSelection( ff.print(seqs)), this);\r
     Desktop.jalviewClipboard = new Object[]{seqs,  viewport.alignment.getDataset()};\r
@@ -830,7 +828,10 @@ public class AlignFrame
         //!newAlignment\r
         for (int i = 0; i < sequences.length; i++)\r
         {\r
-          viewport.alignment.addSequence(sequences[i]);\r
+          Sequence newseq = new Sequence(sequences[i].getName(),\r
+              sequences[i].getSequence(), sequences[i].getStart(),\r
+              sequences[i].getEnd());\r
+          viewport.alignment.addSequence(newseq);\r
           if(sequences[i].getDatasetSequence()==null)\r
           {\r
              ////////////////////////////\r
@@ -840,10 +841,8 @@ public class AlignFrame
                                        AlignSeq.extractGaps("-. ", sequences[i].getSequence()),\r
                                        sequences[i].getStart(),\r
                                        sequences[i].getEnd());\r
-            sequences[i].setDatasetSequence(ds);\r
+            newseq.setDatasetSequence(ds);\r
             viewport.alignment.getDataset().addSequence(ds);\r
-\r
-\r
           }\r
 \r
         }\r
@@ -979,6 +978,7 @@ public class AlignFrame
     viewport.setSelectionGroup(null);\r
     viewport.getColumnSelection().clear();\r
     viewport.setSelectionGroup(null);\r
+    alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);\r
     alignPanel.annotationPanel.activeRes = null;\r
     PaintRefresher.Refresh(null, viewport.alignment);\r
   }\r
@@ -1206,16 +1206,6 @@ public class AlignFrame
    if(alignPanel.overviewPanel!=null)\r
      alignPanel.overviewPanel.updateOverviewImage();\r
 \r
-  Provenance prov = viewport.alignment.getProvenance();\r
-  if(prov == null)\r
-   {\r
-     prov = new Provenance();\r
-     viewport.alignment.setProvenance(prov);\r
-   }\r
-\r
-   prov.addEntry("Me",\r
-       "Edited in Jalview", new java.util.Date(), "myID");\r
-\r
    alignPanel.repaint();\r
  }\r
 \r
@@ -1322,14 +1312,6 @@ public class AlignFrame
     alignPanel.repaint();\r
   }\r
 \r
-  public void seqDBRef_actionPerformed(ActionEvent e)\r
-  {\r
-    viewport.setShowDBPrefix(seqDBRef.isSelected());\r
-\r
-    alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());\r
-    alignPanel.repaint();\r
-  }\r
-\r
 \r
   /**\r
    * DOCUMENT ME!\r
@@ -1432,10 +1414,8 @@ public class AlignFrame
   {\r
     viewport.showSequenceFeatures(sequenceFeatures.isSelected());\r
 \r
-    if (viewport.showSequenceFeatures &&\r
-        ! ( (Alignment) viewport.alignment.getDataset()).featuresAdded)\r
+    if (viewport.showSequenceFeatures)\r
     {\r
-      System.out.println("new fetcher");\r
       new SequenceFeatureFetcher(viewport.\r
          alignment,\r
           alignPanel);\r
@@ -1918,7 +1898,7 @@ public class AlignFrame
   {\r
     addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,\r
                                    HistoryItem.SORT));\r
-    AlignmentSorter.sortByID(viewport.getAlignment(), viewport.showDBPrefix);\r
+    AlignmentSorter.sortByID(viewport.getAlignment());\r
     alignPanel.repaint();\r
   }\r
 \r
@@ -2228,7 +2208,16 @@ public class AlignFrame
   {\r
     SequenceI seq = null;\r
     SequenceI[] msa = null;\r
+/*\r
+         if (predictindex==-1) {\r
 \r
+          JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+                                                "The alignment contains no columns or residues usable for prediction!",\r
+                                                "Invalid Alignment Selection", JOptionPane.WARNING_MESSAGE);\r
+          this.\r
+          return;\r
+        }\r
+*/\r
     if ( (viewport.getSelectionGroup() != null) &&\r
         (viewport.getSelectionGroup().getSize() > 0))\r
     {\r
@@ -2459,7 +2448,18 @@ public class AlignFrame
           {\r
             public void actionPerformed(ActionEvent e)\r
             {\r
-              SequenceI[] msa = gatherSeqOrMsaForSecStrPrediction();\r
+              SequenceI[] msa = SeqsetUtils.getNonEmptySequenceSet(gatherSeqOrMsaForSecStrPrediction());\r
+              if (msa==null) {\r
+                JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+                    "There are no columns or residues usable for prediction!\n"\r
+                    +"There must be valid residues in at least one\n"\r
+                    +"of the sequences in the alignment,\n"\r
+                    +"or in the currently selected region.",\r
+                    "Invalid Input for Secondary Structure Prediction",\r
+                    JOptionPane.WARNING_MESSAGE);\r
+                return;\r
+              }\r
+\r
               if (msa.length == 1)\r
               {\r
                 // Single Sequence prediction\r
@@ -2469,7 +2469,7 @@ public class AlignFrame
               {\r
                 if (msa.length > 1)\r
                 {\r
-                  // Single Sequence prediction\r
+                  // Aligned Sequences prediction\r
                   jalview.ws.JPredClient ct = new jalview.ws.JPredClient(sh,\r
                       title, msa);\r
                 }\r