//!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
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
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
{\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
{\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
{\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