public class AlignFrame extends GAlignFrame implements DropTargetListener,
IProgressIndicator
{
+
/** DOCUMENT ME!! */
public static final int DEFAULT_WIDTH = 700;
String fileName = null;
/**
- * Creates a new AlignFrame object.
+ * Creates a new AlignFrame object with specific width and height.
*
* @param al
- * DOCUMENT ME!
+ * @param width
+ * @param height
*/
public AlignFrame(AlignmentI al, int width, int height)
{
this(al, null, width, height);
}
-
+ /**
+ * Creates a new AlignFrame object with specific width, height and sequenceSetId
+ * @param al
+ * @param width
+ * @param height
+ * @param sequenceSetId
+ */
+ public AlignFrame(AlignmentI al, int width, int height, String sequenceSetId)
+ {
+ this(al, null, width, height, sequenceSetId);
+ }
+ /**
+ * Creates a new AlignFrame object with specific width, height and sequenceSetId
+ * @param al
+ * @param width
+ * @param height
+ * @param sequenceSetId
+ * @param viewId
+ */
+ public AlignFrame(AlignmentI al, int width, int height, String sequenceSetId, String viewId)
+ {
+ this(al, null, width, height, sequenceSetId, viewId);
+ }
/**
* new alignment window with hidden columns
*
* AlignmentI
* @param hiddenColumns
* ColumnSelection or null
+ * @param width Width of alignment frame
+ * @param height height of frame.
*/
public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
int width, int height)
{
- this.setSize(width, height);
- viewport = new AlignViewport(al, hiddenColumns);
+ this(al, hiddenColumns, width, height, null);
+ }
+ /**
+ * Create alignment frame for al with hiddenColumns, a specific width and height, and specific sequenceId
+ * @param al
+ * @param hiddenColumns
+ * @param width
+ * @param height
+ * @param sequenceSetId (may be null)
+ */
+ public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
+ int width, int height, String sequenceSetId)
+ {
+ this(al, hiddenColumns, width, height, sequenceSetId, null);
+ }
+
+ /**
+ * Create alignment frame for al with hiddenColumns, a specific width and height, and specific sequenceId
+ * @param al
+ * @param hiddenColumns
+ * @param width
+ * @param height
+ * @param sequenceSetId (may be null)
+ * @param viewId (may be null)
+ */
+ public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns, int width, int height,
+ String sequenceSetId, String viewId)
+ {
+ setSize(width, height);
+ viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
alignPanel = new AlignmentPanel(this, viewport);
addAlignmentPanel(ap, false);
init();
}
-
+ /**
+ * initalise the alignframe from the underlying viewport data and the configurations
+ */
void init()
{
if (viewport.conservation == null)
annotationPanelMenuItem.setState(av.showAnnotation);
viewBoxesMenuItem.setSelected(av.showBoxes);
viewTextMenuItem.setSelected(av.showText);
-
+ showUnconservedMenuItem.setSelected(av.showUnconserved);
setColourSelected(ColourSchemeProperty.getColourName(av
.getGlobalColourScheme()));
updateEditMenuBar();
}
- Hashtable progressBars;
+ Hashtable progressBars, progressBarHandlers;
/*
* (non-Javadoc)
if (progressBars == null)
{
progressBars = new Hashtable();
+ progressBarHandlers = new Hashtable();
}
JPanel progressPanel;
{
statusBar.setText(message);
}
-
+ if (progressBarHandlers.contains(new Long(id)))
+ {
+ progressBarHandlers.remove(new Long(id));
+ }
layout.setRows(layout.getRows() - 1);
}
else
setMenusForViewport();
validate();
}
+ public void registerHandler(final long id, final IProgressIndicatorHandler handler)
+ {
+ if (progressBarHandlers==null || !progressBars.contains(new Long(id)))
+ {
+ throw new Error("call setProgressBar before registering the progress bar's handler.");
+ }
+ progressBarHandlers.put(new Long(id), handler);
+ final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
+ if (handler.canCancel())
+ {
+ JButton cancel = new JButton("Cancel");
+ final IProgressIndicator us=this;
+ cancel.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e)
+ {
+ handler.cancelActivity(id);
+ us.setProgressBar("Cancelled "+((JLabel)progressPanel.getComponent(0)).getText(), id);
+ }
+ });
+ progressPanel.add(cancel, BorderLayout.EAST);
+ }
+ }
/**
*
* @return true if any progress bars are still active
public void save_actionPerformed(ActionEvent e)
{
if (fileName == null
- || (currentFileFormat == null || jalview.io.AppletFormatAdapter
- .isValidFormat(currentFileFormat, true))
+ || (currentFileFormat == null
+ || !jalview.io.FormatAdapter.isValidIOFormat(currentFileFormat, true))
|| fileName.startsWith("http"))
{
saveAs_actionPerformed(null);
}
/**
- * DOCUMENT ME!
+ * Close the current view or all views in the alignment frame.
+ * If the frame only contains one view then the alignment will be removed from memory.
*
- * @param e
- * DOCUMENT ME!
+ * @param closeAllTabs
*/
public void closeMenuItem_actionPerformed(boolean closeAllTabs)
{
for (int i = 0; i < alignPanels.size(); i++)
{
AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
- jalview.structure.StructureSelectionManager
- .getStructureSelectionManager()
- .removeStructureViewerListener(ap.seqPanel, null);
+ jalview.structure.StructureSelectionManager ssm =
+ jalview.structure.StructureSelectionManager
+ .getStructureSelectionManager();
+ ssm.removeStructureViewerListener(ap.seqPanel, null);
+ ssm.removeSelectionListener(ap.seqPanel);
PaintRefresher.RemoveComponent(ap.seqPanel.seqCanvas);
PaintRefresher.RemoveComponent(ap.idPanel.idCanvas);
PaintRefresher.RemoveComponent(ap);
}
else
{
- int index = tabbedPane.getSelectedIndex();
-
- alignPanels.removeElement(alignPanel);
- PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
- PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
- PaintRefresher.RemoveComponent(alignPanel);
- viewport.alignment = null;
- alignPanel = null;
+ closeView(alignPanel);
viewport = null;
-
- tabbedPane.removeTabAt(index);
- tabbedPane.validate();
-
- if (index == tabbedPane.getTabCount())
- {
- index--;
- }
-
- this.tabSelectionChanged(index);
}
}
}
}
+ public void closeView(AlignmentPanel alignPanel2)
+ {
+ int index = tabbedPane.getSelectedIndex();
+ int closedindex = tabbedPane.indexOfComponent(alignPanel2);
+ alignPanels.removeElement(alignPanel2);
+ PaintRefresher.RemoveComponent(alignPanel2.seqPanel.seqCanvas);
+ PaintRefresher.RemoveComponent(alignPanel2.idPanel.idCanvas);
+ PaintRefresher.RemoveComponent(alignPanel2);
+ alignPanel2.av.alignment = null;
+
+ if (viewport == alignPanel2.av)
+ {
+ viewport = null;
+ }
+ alignPanel2 = null;
+
+ tabbedPane.removeTabAt(closedindex);
+ tabbedPane.validate();
+
+ if (index > closedindex || index == tabbedPane.getTabCount())
+ {
+ // modify currently selected tab index if necessary.
+ index--;
+ }
+
+ this.tabSelectionChanged(index);
+ }
+
/**
* DOCUMENT ME!
*/
viewport.alignment));
viewport.setSelectionGroup(null);
+ viewport.sendSelection();
viewport.alignment.deleteGroup(sg);
viewport.firePropertyChange("alignment", null, viewport.getAlignment()
.getSequences());
-
if (viewport.getAlignment().getHeight() < 1)
{
try
sg.setEndRes(viewport.alignment.getWidth() - 1);
viewport.setSelectionGroup(sg);
+ viewport.sendSelection();
alignPanel.paintAlignment(true);
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
}
}
alignPanel.paintAlignment(true);
-
+ viewport.sendSelection();
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
}
public void padGapsMenuitem_actionPerformed(ActionEvent e)
{
viewport.padGaps = padGapsMenuitem.isSelected();
-
viewport.firePropertyChange("alignment", null, viewport.getAlignment()
.getSequences());
}
-
+
+ //else
+ {
+ // if (justifySeqs>0)
+ {
+ // alignment.justify(justifySeqs!=RIGHT_JUSTIFY);
+ }
+ }
+ //}
+
/**
* DOCUMENT ME!
*
newap.av.viewName = newViewName;
- addAlignmentPanel(newap, false);
+ addAlignmentPanel(newap, true);
if (alignPanels.size() == 2)
{
viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();
alignPanel.paintAlignment(true);
}
+ /* (non-Javadoc)
+ * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
+ */
+ protected void followHighlight_actionPerformed()
+ {
+ if (viewport.followHighlight = this.followHighlightMenuItem.getState())
+ {
+ alignPanel.scrollToPosition(alignPanel.seqPanel.seqCanvas.searchResults, false);
+ }
+ }
/**
* DOCUMENT ME!
}
/**
- * DOCUMENT ME!
+ * Set or clear 'Show Sequence Features'
*
* @param evt
* DOCUMENT ME!
alignPanel.getOverviewPanel().updateOverviewImage();
}
}
+ /**
+ * Set or clear 'Show Sequence Features'
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
+ {
+ viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight.isSelected());
+ if (viewport.getShowSequenceFeaturesHeight())
+ {
+ // ensure we're actually displaying features
+ viewport.setShowSequenceFeatures(true);
+ showSeqFeatures.setSelected(true);
+ }
+ alignPanel.paintAlignment(true);
+ if (alignPanel.getOverviewPanel() != null)
+ {
+ alignPanel.getOverviewPanel().updateOverviewImage();
+ }
+ }
/**
* DOCUMENT ME!
addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
alignPanel.paintAlignment(true);
}
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void sortLengthMenuItem_actionPerformed(ActionEvent e)
+ {
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+ AlignmentSorter.sortByLength(viewport.getAlignment());
+ addHistoryItem(new OrderCommand("Length Sort", oldOrder, viewport.alignment));
+ alignPanel.paintAlignment(true);
+ }
/**
* DOCUMENT ME!
private void resetWebServiceMenu()
{
webService.removeAll();
- // Temporary hack - DBRef Fetcher always top level ws entry.
- JMenuItem rfetch = new JMenuItem("Fetch DB References");
- rfetch
- .setToolTipText("Retrieve and parse sequence database records for the alignment or the currently selected sequences");
- webService.add(rfetch);
- rfetch.addActionListener(new ActionListener()
- {
-
- public void actionPerformed(ActionEvent e)
- {
- new Thread(new Runnable()
- {
-
- public void run()
- {
- new jalview.ws.DBRefFetcher(alignPanel.av
- .getSequenceSelection(), alignPanel.alignFrame)
- .fetchDBRefs(false);
- }
- }).start();
-
- }
-
- });
+ build_fetchdbmenu(webService);
}
/*
showProducts.removeAll();
final boolean dna = viewport.getAlignment().isNucleotide();
final Alignment ds = dataset;
- String[] ptypes = CrossRef.findSequenceXrefTypes(dna, selection,
+ String[] ptypes = (selection==null || selection.length==0) ? null
+ : CrossRef.findSequenceXrefTypes(dna, selection,
dataset);
// Object[] prods =
// CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
}
Alignment al = new Alignment(sprods);
AlignedCodonFrame[] cf = prods.getCodonFrames();
+ al.setDataset(ds);
for (int s = 0; cf != null && s < cf.length; s++)
{
al.addCodonFrame(cf[s]);
cf[s] = null;
}
- al.setDataset(ds);
AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
DEFAULT_HEIGHT);
String newtitle = "" + ((fdna) ? "Proteins " : "Nucleotides ")
{
viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected());
}
+
+ /**
+ * find the viewport amongst the tabs in this alignment frame and close that tab
+ * @param av
+ */
+ public boolean closeView(AlignViewport av)
+ {
+ if (viewport == av)
+ {
+ this.closeMenuItem_actionPerformed(false);
+ return true;
+ }
+ Component[] comp = tabbedPane.getComponents();
+ for (int i=0;comp!=null && i<comp.length;i++)
+ {
+ if (comp[i] instanceof AlignmentPanel)
+ {
+ if (((AlignmentPanel) comp[i]).av == av)
+ {
+ // close the view.
+ closeView((AlignmentPanel) comp[i]);
+ return true;
+ }
+ }
+ }
+ return false;
+ }
+ protected void build_fetchdbmenu(JMenu webService) {
+ // Temporary hack - DBRef Fetcher always top level ws entry.
+ // TODO We probably want to store a sequence database checklist in preferences and have checkboxes.. rather than individual sources selected here
+ JMenu rfetch = new JMenu("Fetch DB References");
+ rfetch
+ .setToolTipText("Retrieve and parse sequence database records for the alignment or the currently selected sequences");
+ webService.add(rfetch);
+
+ JMenuItem fetchr = new JMenuItem("Standard Databases");
+ fetchr.setToolTipText("Fetch from EMBL/EMBLCDS or Uniprot/PDB and any selected DAS sources");
+ fetchr.addActionListener(new ActionListener()
+ {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ new Thread(new Runnable()
+ {
+
+ public void run()
+ {
+ new jalview.ws.DBRefFetcher(alignPanel.av
+ .getSequenceSelection(), alignPanel.alignFrame)
+ .fetchDBRefs(false);
+ }
+ }).start();
+
+ }
+
+ });
+ rfetch.add(fetchr);
+ JMenu dfetch = new JMenu();
+ rfetch.add(dfetch);
+ jalview.ws.SequenceFetcher sf = SequenceFetcher.getSequenceFetcherSingleton(this);
+ String[] otherdb = sf.getOrderedSupportedSources();
+ // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
+ // jalview.util.QuickSort.sort(otherdb, otherdb);
+ int comp=0,mcomp=15;
+ String mname=null;
+ if (otherdb!=null && otherdb.length>0)
+ {
+ for (int i=0; i<otherdb.length; i++)
+ {
+ String dbname =sf.getSourceProxy(otherdb[i]).getDbName();
+ if (mname == null)
+ {
+ mname = "from '"+dbname+"'";
+ }
+ fetchr = new JMenuItem(otherdb[i]);
+ final String[] dassource = new String[] { otherdb[i] };
+ fetchr.addActionListener(new ActionListener()
+ {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ new Thread(new Runnable()
+ {
+
+ public void run()
+ {
+ new jalview.ws.DBRefFetcher(alignPanel.av
+ .getSequenceSelection(), alignPanel.alignFrame, dassource)
+ .fetchDBRefs(false);
+ }
+ }).start();
+ }
+
+ });
+ fetchr.setToolTipText("Retrieve from "+dbname);
+ dfetch.add(fetchr);
+ if (comp++==mcomp || i==(otherdb.length-1))
+ {
+ dfetch.setText(mname+" to '"+dbname+"'");
+ rfetch.add(dfetch);
+ dfetch = new JMenu();
+ mname = null;
+ comp=0;
+ }
+ }
+ }
+ }
+ /**
+ * Left justify the whole alignment.
+ */
+ protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
+ {
+ AlignmentI al = viewport.getAlignment();
+ al.justify(false);
+ viewport.firePropertyChange("alignment", null, al);
+ }
+ /**
+ * Right justify the whole alignment.
+ */
+ protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
+ {
+ AlignmentI al = viewport.getAlignment();
+ al.justify(true);
+ viewport.firePropertyChange("alignment", null, al);
+ }
+ public void setShowSeqFeatures(boolean b)
+ {
+ showSeqFeatures.setSelected(true);
+ viewport.setShowSequenceFeatures(true);
+ }
+ /* (non-Javadoc)
+ * @see jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.awt.event.ActionEvent)
+ */
+ protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
+ {
+ viewport.setShowUnconserved(showUnconservedMenuItem.getState());
+ alignPanel.paintAlignment(true);
+ }
}
class PrintThread extends Thread
git://source.jalview.org / jalview.git / blobdiff