import java.awt.dnd.*;\r
import org.biojava.dasobert.eventmodel.*;\r
\r
-\r
/**\r
* DOCUMENT ME!\r
*\r
Stack redoList = new Stack();\r
private int treeCount = 0;\r
\r
-\r
/**\r
- * Creates a new AlignFrame object.\r
- *\r
- * @param al DOCUMENT ME!\r
+ * new alignment window with hidden columns\r
+ * @param al AlignmentI\r
+ * @param hiddenColumns ColumnSelection or null\r
*/\r
- public AlignFrame(AlignmentI al)\r
- {\r
- viewport = new AlignViewport(al);\r
+ public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns) {\r
+\r
+ viewport = new AlignViewport(al, hiddenColumns);\r
\r
this.setDropTarget(new java.awt.dnd.DropTarget(this, this));\r
\r
\r
}\r
\r
+\r
+ /**\r
+ * Creates a new AlignFrame object.\r
+ *\r
+ * @param al DOCUMENT ME!\r
+ */\r
+ public AlignFrame(AlignmentI al)\r
+ {\r
+ this(al, null);\r
+ }\r
+\r
public AlignViewport getViewport()\r
{\r
return viewport;\r
{\r
alignPanel.seqPanel.seqCanvas.fr.featuresAdded();\r
alignPanel.repaint();\r
- if(featureSettings!=null)\r
- featureSettings.setTableData();\r
}\r
}\r
\r
\r
if (viewport.hasHiddenColumns)\r
{\r
- System.out.println("PROMPT USER HERE");\r
- omitHidden = viewport.getSelectionAsString();\r
+ int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,\r
+ "The Alignment contains hidden columns."\r
+ + "\nDo you want to save only the visible alignment?",\r
+ "Save / Omit Hidden Columns",\r
+ JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);\r
+\r
+ if (reply == JOptionPane.YES_OPTION)\r
+ omitHidden = viewport.getViewAsString(false);\r
}\r
\r
String output = new FormatAdapter().formatSequences(\r
format,\r
- viewport.getSelectionAsNewSequence(),\r
- omitHidden) ;\r
-\r
-\r
+ viewport.alignment.getSequencesArray(),\r
+ omitHidden);\r
\r
if (output == null)\r
{\r
*/\r
protected void outputText_actionPerformed(ActionEvent e)\r
{\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
-\r
-\r
String [] omitHidden = null;\r
\r
if(viewport.hasHiddenColumns)\r
{\r
- System.out.println("PROMPT USER HERE");\r
- omitHidden = viewport.getSelectionAsString();\r
+ int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,\r
+ "The Alignment contains hidden columns."\r
+ +"\nDo you want to output only the visible alignment?",\r
+ "Save / Omit Hidden Columns",\r
+ JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);\r
+\r
+ if(reply==JOptionPane.YES_OPTION)\r
+ {\r
+ omitHidden = viewport.getViewAsString(false);\r
+ }\r
}\r
\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
+ Desktop.addInternalFrame(cap,\r
+ "Alignment output - " + e.getActionCommand(), 600,\r
+ 500);\r
+\r
+\r
cap.setText(new FormatAdapter().formatSequences(\r
e.getActionCommand(),\r
- viewport.getSelectionAsNewSequence(),\r
+ viewport.alignment.getSequencesArray(),\r
omitHidden));\r
}\r
\r
new AnnotationExporter().exportFeatures(alignPanel);\r
}\r
\r
+\r
public void exportAnnotations_actionPerformed(ActionEvent e)\r
{\r
new AnnotationExporter().exportAnnotations(\r
}\r
\r
SequenceI [] seqs = viewport.getSelectionAsNewSequence();\r
+ String[] omitHidden = null;\r
\r
- Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
+ if (viewport.hasHiddenColumns)\r
+ {\r
+ omitHidden = viewport.getViewAsString(true);\r
+ }\r
\r
- FastaFile ff = new FastaFile();\r
- ff.addJVSuffix( viewport.showJVSuffix );\r
+ String output = new FormatAdapter().formatSequences(\r
+ "Fasta",\r
+ seqs,\r
+ omitHidden);\r
\r
- c.setContents(new StringSelection(ff.print(seqs)), Desktop.instance);\r
+\r
+ Toolkit.getDefaultToolkit().getSystemClipboard()\r
+ .setContents(new StringSelection(output), Desktop.instance);\r
\r
Vector hiddenColumns = null;\r
- if(viewport.hasHiddenColumns && viewport.getSelectionGroup()!=null)\r
+ if(viewport.hasHiddenColumns)\r
{\r
hiddenColumns =new Vector();\r
int hiddenOffset = viewport.getSelectionGroup().getStartRes();\r
region[1]-hiddenOffset});\r
}\r
}\r
+\r
Desktop.jalviewClipboard = new Object[]{ seqs,\r
viewport.alignment.getDataset(),\r
hiddenColumns};\r
String format = new IdentifyFile().Identify(str, "Paste");\r
SequenceI[] sequences;\r
\r
+\r
if(Desktop.jalviewClipboard!=null)\r
{\r
// The clipboard was filled from within Jalview, we must use the sequences\r
alignment.setDataset( (Alignment)Desktop.jalviewClipboard[1] );\r
else\r
alignment.setDataset( null );\r
+\r
}\r
else\r
{\r
//!newAlignment\r
for (int i = 0; i < sequences.length; i++)\r
{\r
-\r
Sequence newseq = new Sequence(sequences[i].getName(),\r
sequences[i].getSequence(), sequences[i].getStart(),\r
sequences[i].getEnd());\r
\r
alignment.addSequence(newseq);\r
}\r
+\r
+\r
viewport.setEndSeq(alignment.getHeight());\r
alignment.getWidth();\r
viewport.firePropertyChange("alignment", null, alignment.getSequences());\r
}\r
\r
+\r
+\r
+\r
+\r
// Add any annotations attached to sequences\r
for (int i = 0; i < sequences.length; i++)\r
{\r
AlignFrame af = new AlignFrame(alignment);\r
String newtitle = new String("Copied sequences");\r
\r
- if(Desktop.jalviewClipboard[2]!=null)\r
+ if(Desktop.jalviewClipboard!=null && Desktop.jalviewClipboard[2]!=null)\r
{\r
Vector hc = (Vector)Desktop.jalviewClipboard[2];\r
for(int i=0; i<hc.size(); i++)\r
{\r
int [] region = (int[]) hc.elementAt(i);\r
- for(int j=region[0]; j<region[1]+1; j++)\r
- af.viewport.getColumnSelection().addElement(j);\r
- af.viewport.getColumnSelection().hideColumns(region[0], af.viewport);\r
+ af.viewport.hideColumns(region[0], region[1]);\r
}\r
}\r
\r
PaintRefresher.Refresh(null, viewport.alignment);\r
}\r
\r
+ public void invertColSel_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.invertColumnSelection();\r
+ alignPanel.repaint();\r
+ }\r
+\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
alignPanel.setWrapAlignment(wrapMenuItem.isSelected());\r
}\r
\r
+ public void showAllSeqs_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.showAllHiddenSeqs();\r
+ repaint();\r
+ }\r
+\r
+ public void showAllColumns_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.showAllHiddenColumns();\r
+ }\r
+\r
+ public void hideSelSequences_actionPerformed(ActionEvent e)\r
+ {\r
+ if(viewport.getSelectionGroup()==null)\r
+ return;\r
+\r
+ SequenceI [] seqs = viewport.getSelectionGroup().getSequencesInOrder(\r
+ viewport.alignment\r
+ );\r
+\r
+ for(int i=0; i<seqs.length; i++)\r
+ {\r
+ viewport.hideSequence(seqs[i]);\r
+ }\r
+\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ public void hideSelColumns_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.hideSelectedColumns();\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ public void hiddenMarkers_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());\r
+ repaint();\r
+ }\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
}\r
\r
\r
- FeatureSettings featureSettings;\r
+ public FeatureSettings featureSettings;\r
public void featureSettings_actionPerformed(ActionEvent e)\r
{\r
if(featureSettings !=null )\r
return;\r
}\r
\r
+ if(viewport.alignment.getHeight()<2)\r
+ return;\r
+\r
tp = new TreePanel(viewport, type, pwType);\r
}\r
\r
* or just the selected set will be submitted for multiple alignment.\r
*\r
*/\r
- private SequenceI[] gatherSequencesForAlignment()\r
+ private jalview.datamodel.AlignmentView gatherSequencesForAlignment()\r
{\r
// Now, check we have enough sequences\r
- SequenceI[] msa = null;\r
+ AlignmentView msa = null;\r
\r
if ( (viewport.getSelectionGroup() != null) &&\r
(viewport.getSelectionGroup().getSize(false) > 1))\r
{\r
// JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!\r
- SequenceGroup seqs = viewport.getSelectionGroup();\r
+ /*SequenceGroup seqs = viewport.getSelectionGroup();\r
int sz;\r
msa = new SequenceI[sz = seqs.getSize(false)];\r
\r
for (int i = 0; i < sz; i++)\r
{\r
msa[i] = (SequenceI) seqs.getSequenceAt(i);\r
- }\r
+ } */\r
+ msa = viewport.getAlignmentView(true);\r
}\r
else\r
{\r
- Vector seqs = viewport.getAlignment().getSequences();\r
+ /*Vector seqs = viewport.getAlignment().getSequences();\r
\r
if (seqs.size() > 1)\r
{\r
{\r
msa[i] = (SequenceI) seqs.elementAt(i);\r
}\r
- }\r
+ }*/\r
+ msa = viewport.getAlignmentView(false);\r
}\r
return msa;\r
}\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- SequenceI[] msa = gatherSequencesForAlignment();\r
+ AlignmentView msa = gatherSequencesForAlignment();\r
new jalview.ws.MsaWSClient(sh, title, msa,\r
false, true, viewport.getAlignment().getDataset(), af);\r
\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- SequenceI[] msa = gatherSequencesForAlignment();\r
+ AlignmentView msa = gatherSequencesForAlignment();\r
new jalview.ws.MsaWSClient(sh, title, msa,\r
true, true, viewport.getAlignment().getDataset(), af);\r
\r
\r
\r
\r
-\r
public void showTranslation_actionPerformed(ActionEvent e)\r
{\r
- int s, sSize = viewport.alignment.getHeight();\r
+ SequenceI [] selection = viewport.getSelectionAsNewSequence();\r
+ String [] seqstring = viewport.getViewAsString(true);\r
+\r
+ int s, sSize = selection.length;\r
SequenceI [] newSeq = new SequenceI[sSize];\r
\r
int res, resSize;\r
for(s=0; s<sSize; s++)\r
{\r
protein = new StringBuffer();\r
- seq = AlignSeq.extractGaps("-. ", viewport.alignment.getSequenceAt(s).getSequence());\r
+ seq = AlignSeq.extractGaps("-. ", seqstring[s]);\r
resSize = seq.length();\r
resSize -= resSize%3;\r
\r
else\r
protein.append( aa );\r
}\r
- newSeq[s] = new Sequence(viewport.alignment.getSequenceAt(s).getName(), protein.toString());\r
+ newSeq[s] = new Sequence(selection[s].getName(),\r
+ protein.toString());\r
}\r
\r
\r
AppletFormatAdapter.FILE);\r
if (!isGroupsFile)\r
{\r
- String protocol = "File";\r
- String format = new IdentifyFile().Identify(file, protocol);\r
- SequenceI[] sequences = new FormatAdapter().readFile(file, protocol,\r
- format);\r
-\r
- FastaFile ff = new FastaFile();\r
- Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
- c.setContents(new StringSelection(ff.print(sequences)), Desktop.instance);\r
-\r
- this.paste(false);\r
+ String format = new IdentifyFile().Identify(file, FormatAdapter.FILE);\r
+ new FileLoader().LoadFile(viewport, file, FormatAdapter.FILE, format);\r
}\r
}\r
else\r
git://source.jalview.org / jalview.git / blobdiff