*/
package jalview.appletgui;
+import java.awt.BorderLayout;
+import java.awt.Canvas;
+import java.awt.CheckboxMenuItem;
+import java.awt.Color;
+import java.awt.FlowLayout;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Frame;
+import java.awt.Graphics;
+import java.awt.Label;
+import java.awt.Menu;
+import java.awt.MenuBar;
+import java.awt.MenuItem;
+import java.awt.Panel;
+import java.awt.Rectangle;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.FocusEvent;
+import java.awt.event.FocusListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.KeyEvent;
+import java.awt.event.KeyListener;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
+import java.io.IOException;
+import java.io.UnsupportedEncodingException;
+import java.net.URL;
+import java.net.URLEncoder;
+import java.util.Arrays;
+import java.util.Deque;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.StringTokenizer;
+import java.util.Vector;
+
+import org.jmol.viewer.Viewer;
+
import jalview.analysis.AlignmentSorter;
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.analysis.TreeBuilder;
import jalview.viewmodel.AlignmentViewport;
import jalview.viewmodel.ViewportRanges;
-import java.awt.BorderLayout;
-import java.awt.Canvas;
-import java.awt.CheckboxMenuItem;
-import java.awt.Color;
-import java.awt.FlowLayout;
-import java.awt.Font;
-import java.awt.FontMetrics;
-import java.awt.Frame;
-import java.awt.Graphics;
-import java.awt.Label;
-import java.awt.Menu;
-import java.awt.MenuBar;
-import java.awt.MenuItem;
-import java.awt.Panel;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.FocusEvent;
-import java.awt.event.FocusListener;
-import java.awt.event.ItemEvent;
-import java.awt.event.ItemListener;
-import java.awt.event.KeyEvent;
-import java.awt.event.KeyListener;
-import java.awt.event.WindowAdapter;
-import java.awt.event.WindowEvent;
-import java.io.IOException;
-import java.net.URL;
-import java.net.URLEncoder;
-import java.util.Arrays;
-import java.util.Deque;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.StringTokenizer;
-import java.util.Vector;
-
-import org.jmol.viewer.Viewer;
-
public class AlignFrame extends EmbmenuFrame implements ActionListener,
ItemListener, KeyListener, AlignViewControllerGuiI
{
createAlignFrameWindow(embedded);
validate();
alignPanel.adjustAnnotationHeight();
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, true);
}
public AlignViewport getAlignViewport()
{
viewport.featureSettings.refreshTable();
}
- alignPanel.paintAlignment(true);
- statusBar.setText(MessageManager
+ alignPanel.paintAlignment(true, true);
+ setStatus(MessageManager
.getString("label.successfully_added_features_alignment"));
}
return featuresFile;
case KeyEvent.VK_F2:
viewport.cursorMode = !viewport.cursorMode;
- statusBar.setText(MessageManager
- .formatMessage("label.keyboard_editing_mode", new String[]
+ setStatus(MessageManager.formatMessage("label.keyboard_editing_mode",
+ new String[]
{ (viewport.cursorMode ? "on" : "off") }));
if (viewport.cursorMode)
{
break;
}
- alignPanel.paintAlignment(true);
+ // TODO: repaint flags set only if the keystroke warrants it
+ alignPanel.paintAlignment(true, true);
}
/**
{
applyAutoAnnotationSettings_actionPerformed();
}
- alignPanel.paintAlignment(true);
+ // TODO: repaint flags set only if warranted
+ alignPanel.paintAlignment(true, true);
}
/**
else if (source == invertColSel)
{
viewport.invertColumnSelection();
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(false, false);
viewport.sendSelection();
}
else if (source == remove2LeftMenuItem)
else if (source == showColumns)
{
viewport.showAllHiddenColumns();
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, true);
viewport.sendSelection();
}
else if (source == showSeqs)
{
viewport.showAllHiddenSeqs();
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, true);
// uncomment if we want to slave sequence selections in split frame
// viewport.sendSelection();
}
else if (source == hideColumns)
{
viewport.hideSelectedColumns();
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, true);
viewport.sendSelection();
}
else if (source == hideSequences
&& viewport.getSelectionGroup() != null)
{
viewport.hideAllSelectedSeqs();
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, true);
// uncomment if we want to slave sequence selections in split frame
// viewport.sendSelection();
}
else if (source == hideAllButSelection)
{
toggleHiddenRegions(false, false);
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, true);
viewport.sendSelection();
}
else if (source == hideAllSelection)
viewport.expandColSelection(sg, false);
viewport.hideAllSelectedSeqs();
viewport.hideSelectedColumns();
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, true);
viewport.sendSelection();
}
else if (source == showAllHidden)
{
viewport.showAllHiddenColumns();
viewport.showAllHiddenSeqs();
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, true);
viewport.sendSelection();
}
else if (source == showGroupConsensus)
}
else if (source == featureSettings)
{
- new FeatureSettings(alignPanel);
+ showFeatureSettingsUI();
}
else if (source == alProperties)
{
FeaturesFile formatter = new FeaturesFile();
if (format.equalsIgnoreCase("Jalview"))
{
- features = formatter.printJalviewFormat(viewport.getAlignment()
- .getSequencesArray(), getDisplayedFeatureCols(),
- getDisplayedFeatureGroups(), true);
+ features = formatter.printJalviewFormat(
+ viewport.getAlignment().getSequencesArray(),
+ alignPanel.getFeatureRenderer(), true, false);
}
else
{
- features = formatter.printGffFormat(viewport.getAlignment()
- .getSequencesArray(), getDisplayedFeatureCols(),
- getDisplayedFeatureGroups(), true);
+ features = formatter.printGffFormat(
+ viewport.getAlignment().getSequencesArray(),
+ alignPanel.getFeatureRenderer(), true, false);
}
if (displayTextbox)
try
{
new URL(url);
- url = URLEncoder.encode(url);
+ url = URLEncoder.encode(url, "UTF-8");
}
/*
* When we finally deprecate 1.1 compatibility, we can start to use
* URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
- * (UnsupportedEncodingException ex) { System.err.println("WARNING -
+ * (UnsupportedEncodingException ex) { jalview.bin.Console.errPrintln("WARNING -
* IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
* ex.printStackTrace(); }
*/
catch (java.net.MalformedURLException ex)
{
url = viewport.applet.getCodeBase() + url;
+ } catch (UnsupportedEncodingException ex)
+ {
+ jalview.bin.Console.errPrintln(
+ "WARNING = IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "
+ + url);
+ ex.printStackTrace();
}
return url;
}
{
System.exit(0);
}
- else
+
+ viewport = null;
+ if (alignPanel != null && alignPanel.overviewPanel != null)
{
+ alignPanel.overviewPanel.dispose();
}
- viewport = null;
alignPanel = null;
this.dispose();
}
}
viewport.getAlignment().moveSelectedSequencesByOne(sg,
up ? null : viewport.getHiddenRepSequences(), up);
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, false);
/*
* Also move cDNA/protein complement sequences
viewport, complement);
complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
up ? null : complement.getHiddenRepSequences(), up);
- getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
+ getSplitFrame().getComplement(this).alignPanel.paintAlignment(true,
+ false);
}
}
static StringBuffer copiedSequences;
- static Vector<int[]> copiedHiddenColumns;
+ static HiddenColumns copiedHiddenColumns;
protected void copy_actionPerformed()
{
if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
{
- copiedHiddenColumns = new Vector<>(viewport.getAlignment()
- .getHiddenColumns().getHiddenColumnsCopy());
int hiddenOffset = viewport.getSelectionGroup().getStartRes();
- for (int[] region : copiedHiddenColumns)
- {
- region[0] = region[0] - hiddenOffset;
- region[1] = region[1] - hiddenOffset;
- }
+ int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
+
+ // create new HiddenColumns object with copy of hidden regions
+ // between startRes and endRes, offset by startRes
+ copiedHiddenColumns = new HiddenColumns(
+ viewport.getAlignment().getHiddenColumns(), hiddenOffset,
+ hiddenCutoff, hiddenOffset);
}
else
{
{
try
{
-
if (copiedSequences == null)
{
return;
}
- StringTokenizer st = new StringTokenizer(copiedSequences.toString());
+ StringTokenizer st = new StringTokenizer(copiedSequences.toString(),
+ "\t");
Vector seqs = new Vector();
while (st.hasMoreElements())
{
}
AlignFrame af = new AlignFrame(new Alignment(newSeqs),
viewport.applet, newtitle, false);
- if (copiedHiddenColumns != null)
- {
- for (int i = 0; i < copiedHiddenColumns.size(); i++)
- {
- int[] region = copiedHiddenColumns.elementAt(i);
- af.viewport.hideColumns(region[0], region[1]);
- }
- }
+ af.viewport.setHiddenColumns(copiedHiddenColumns);
jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
frameHeight);
seqs, 0, viewport.getAlignment().getWidth(),
viewport.getAlignment()));
- viewport.getRanges().setEndSeq(viewport.getAlignment().getHeight());
+ viewport.getRanges().setEndSeq(viewport.getAlignment().getHeight() - 1); // BH
+ // 2019.04.18
viewport.getAlignment().getWidth();
viewport.firePropertyChange("alignment", null,
viewport.getAlignment().getSequences());
{
PaintRefresher.Refresh(this, viewport.getSequenceSetId());
alignPanel.updateAnnotation();
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, true);
}
}
// JAL-2034 - should delegate to
// alignPanel to decide if overview needs
// updating.
- alignPanel.paintAlignment(false);
+ alignPanel.paintAlignment(false, false);
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
viewport.sendSelection();
}
// JAL-2034 - should delegate to
// alignPanel to decide if overview needs
// updating.
- alignPanel.paintAlignment(false);
+ alignPanel.paintAlignment(false, false);
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
viewport.sendSelection();
}
public void invertColSel_actionPerformed()
{
viewport.invertColumnSelection();
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, false);
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
viewport.sendSelection();
}
column, al);
}
- statusBar.setText(MessageManager
- .formatMessage("label.removed_columns", new String[]
+ setStatus(MessageManager.formatMessage("label.removed_columns",
+ new String[]
{ Integer.valueOf(trimRegion.getSize()).toString() }));
addHistoryItem(trimRegion);
addHistoryItem(removeGapCols);
- statusBar.setText(MessageManager
- .formatMessage("label.removed_empty_columns", new String[]
+ setStatus(MessageManager.formatMessage("label.removed_empty_columns",
+ new String[]
{ Integer.valueOf(removeGapCols.getSize()).toString() }));
// This is to maintain viewport position on first residue
{
viewport.setShowJVSuffix(seqLimits.getState());
alignPanel.fontChanged();
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, false);
}
protected void colourTextMenuItem_actionPerformed()
{
viewport.setColourText(colourTextMenuItem.getState());
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(false, false);
}
protected void displayNonconservedMenuItem_actionPerformed()
{
viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(false, false);
}
protected void wrapMenuItem_actionPerformed()
scaleAbove.setEnabled(wrapMenuItem.getState());
scaleLeft.setEnabled(wrapMenuItem.getState());
scaleRight.setEnabled(wrapMenuItem.getState());
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, false);
}
public void overviewMenuItem_actionPerformed()
{
viewport.setGlobalColourScheme(cs);
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, true);
}
protected void modifyPID_actionPerformed()
addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
viewport.getAlignment()));
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, false);
}
public void sortIDMenuItem_actionPerformed()
AlignmentSorter.sortByID(viewport.getAlignment());
addHistoryItem(
new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, false);
}
public void sortLengthMenuItem_actionPerformed()
AlignmentSorter.sortByLength(viewport.getAlignment());
addHistoryItem(new OrderCommand("Length Sort", oldOrder,
viewport.getAlignment()));
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, false);
}
public void sortGroupMenuItem_actionPerformed()
AlignmentSorter.sortByGroup(viewport.getAlignment());
addHistoryItem(new OrderCommand("Group Sort", oldOrder,
viewport.getAlignment()));
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, false);
}
current.insertCharAt(Width - 1, viewport.getGapCharacter());
}
}
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(false, false);
}
if ((viewport.getSelectionGroup() != null
current.insertCharAt(Width - 1, viewport.getGapCharacter());
}
}
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(false, false);
}
addHistoryItem(new OrderCommand(MessageManager
.formatMessage("label.order_by_params", new String[]
{ title }), oldOrder, viewport.getAlignment()));
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, false);
}
/**
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
if (viewport.applet.debug)
{
- System.err.println("Sorting " + alorder.getOrder().size()
+ jalview.bin.Console.errPrintln("Sorting " + alorder.getOrder().size()
+ " in alignment '" + getTitle() + "'");
}
AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
addHistoryItem(new OrderCommand(undoname, oldOrder,
viewport.getAlignment()));
}
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, false);
return true;
}
{
if (viewport.applet == null)
{
- System.out.println("Not running as applet - no browser available.");
+ jalview.bin.Console
+ .outPrintln("Not running as applet - no browser available.");
}
else
{
hydrophobicityColour.setLabel(
MessageManager.getString("label.colourScheme_hydrophobic"));
hydrophobicityColour.addActionListener(this);
- helixColour.setLabel(MessageManager
- .getString("label.colourScheme_helix_propensity"));
+ helixColour.setLabel(
+ MessageManager.getString("label.colourScheme_helixpropensity"));
helixColour.addActionListener(this);
strandColour.setLabel(MessageManager
- .getString("label.colourScheme_strand_propensity"));
+ .getString("label.colourScheme_strandpropensity"));
strandColour.addActionListener(this);
turnColour.setLabel(
- MessageManager.getString("label.colourScheme_turn_propensity"));
+ MessageManager.getString("label.colourScheme_turnpropensity"));
turnColour.addActionListener(this);
buriedColour.setLabel(
- MessageManager.getString("label.colourScheme_buried_index"));
+ MessageManager.getString("label.colourScheme_buriedindex"));
buriedColour.addActionListener(this);
purinePyrimidineColour.setLabel(MessageManager
.getString("label.colourScheme_purine/pyrimidine"));
// .getString("label.rna_interaction"));
// RNAInteractionColour.addActionListener(this);
RNAHelixColour.setLabel(
- MessageManager.getString("label.colourScheme_rna_helices"));
+ MessageManager.getString("label.colourScheme_rnahelices"));
RNAHelixColour.addActionListener(this);
userDefinedColour
.setLabel(MessageManager.getString("action.user_defined"));
userDefinedColour.addActionListener(this);
PIDColour.setLabel(
- MessageManager.getString("label.colourScheme_%_identity"));
+ MessageManager.getString("label.colourScheme_%identity"));
PIDColour.addActionListener(this);
BLOSUM62Colour.setLabel(
MessageManager.getString("label.colourScheme_blosum62"));
BLOSUM62Colour.addActionListener(this);
tcoffeeColour.setLabel(
- MessageManager.getString("label.colourScheme_t-coffee_scores"));
+ MessageManager.getString("label.colourScheme_t-coffeescores"));
// it will be enabled only if a score file is provided
tcoffeeColour.setEnabled(false);
tcoffeeColour.addActionListener(this);
*/
statusBar.setBackground(Color.white);
statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
- statusBar.setText(MessageManager.getString("label.status_bar"));
+ setStatus(MessageManager.getString("label.status_bar"));
this.add(statusBar, BorderLayout.SOUTH);
}
* without an additional javascript library to exchange messages between the
* distinct applets. See http://issues.jalview.org/browse/JAL-621
*
- * @param viewer
+ * @param jmolViewer
* JmolViewer instance
* @param sequenceIds
* - sequence Ids to search for associations
viewer = (Viewer) jmolviewer;
} catch (ClassCastException ex)
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Unsupported viewer object :" + jmolviewer.getClass());
}
if (viewer == null)
{
- System.err.println("Can't use this object as a structure viewer:"
- + jmolviewer.getClass());
+ jalview.bin.Console
+ .errPrintln("Can't use this object as a structure viewer:"
+ + jmolviewer.getClass());
return null;
}
SequenceI[] seqs = null;
chains = (String[]) sqch[1];
if (seqs == null || seqs.length == 0)
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
}
if (protocol == null)
}
if (protocol == null)
{
- System.err.println("Couldn't work out protocol to open structure: "
- + pdb.getId());
+ jalview.bin.Console
+ .errPrintln("Couldn't work out protocol to open structure: "
+ + pdb.getId());
return;
}
}
{
// register the association(s) and quit, don't create any windows.
if (StructureSelectionManager.getStructureSelectionManager(applet)
- .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
+ .setMapping(seqs, chains, pdb.getFile(), protocol,
+ null) == null)
{
- System.err.println("Failed to map " + pdb.getFile() + " ("
- + protocol + ") to any sequences");
+ jalview.bin.Console.errPrintln("Failed to map " + pdb.getFile()
+ + " (" + protocol + ") to any sequences");
}
return;
}
}
if (ajm != null)
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Incremental adding and aligning structure to existing Jmol view not yet implemented.");
// try and add the pdb structure
// ajm.addS
}
else
{
- new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
+ new mc_view.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
}
}
SequenceI[][] seqs, String[][] chains, String[] protocols)
{
// TODO Auto-generated method stub
- System.err.println("Aligned Structure View: Not yet implemented.");
+ jalview.bin.Console
+ .errPrintln("Aligned Structure View: Not yet implemented.");
}
/**
if (!file.isValid())
{
// TODO: raise dialog for gui
- System.err.println("Problems parsing T-Coffee scores: "
+ jalview.bin.Console.errPrintln("Problems parsing T-Coffee scores: "
+ file.getWarningMessage());
- System.err.println("Origin was:\n" + source);
+ jalview.bin.Console.errPrintln("Origin was:\n" + source);
return false;
}
|| aln.getWidth() != file.getWidth()))
{
// TODO: raise a dialog box here rather than bomb out.
- System.err.println(
+ jalview.bin.Console.errPrintln(
"The scores matrix does not match the alignment dimensions");
}
}
else
{
- System.err.println("Problems resolving T-Coffee scores:");
+ jalview.bin.Console.errPrintln("Problems resolving T-Coffee scores:");
if (file.getWarningMessage() != null)
{
- System.err.println(file.getWarningMessage());
+ jalview.bin.Console.errPrintln(file.getWarningMessage());
}
}
return false;
return alignPanel.av.featureSettings;
}
+ @Override
+ public FeatureSettingsControllerI showFeatureSettingsUI()
+ {
+ return new FeatureSettings(alignPanel);
+ }
+
+ private Rectangle fs_bounds = null;
+
+ @Override
+ public void setFeatureSettingsGeometry(Rectangle bounds)
+ {
+ fs_bounds = bounds;
+ }
+
+ @Override
+ public Rectangle getFeatureSettingsGeometry()
+ {
+ return fs_bounds;
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff