/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
*/
package jalview.appletgui;
{
sortPairwiseMenuItem_actionPerformed();
}
+ else if (param.equalsIgnoreCase("Length"))
+ {
+ sortLengthMenuItem_actionPerformed();
+ }
}
param = applet.getParameter("wrap");
* DOCUMENT ME!
*
* @param String
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void parseFeaturesFile(String file, String type)
}
viewport.showSequenceFeatures = true;
sequenceFeatures.setState(true);
- if (viewport.featureSettings!=null)
+ if (viewport.featureSettings != null)
{
viewport.featureSettings.refreshTable();
}
}
alignPanel.paintAlignment(true);
}
+
/**
* called by key handler and the hide all/show all menu items
+ *
* @param toggleSeqs
* @param toggleCols
*/
- private void toggleHiddenRegions(boolean toggleSeqs,
- boolean toggleCols)
+ private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
{
boolean hide = false;
SequenceGroup sg = viewport.getSelectionGroup();
// Hide everything by the current selection - this is a hack - we do the
// invert and then hide
// first check that there will be visible columns after the invert.
- if ((viewport.colSel != null
- && viewport.colSel.getSelected() != null && viewport.colSel
+ if ((viewport.colSel != null && viewport.colSel.getSelected() != null && viewport.colSel
.getSelected().size() > 0)
|| (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
.getEndRes()))
}
}
}
+
public void keyReleased(KeyEvent evt)
{
}
else if (evt.getSource() == this.centreColumnLabelFlag)
{
centreColumnLabelFlag_stateChanged();
- } else if (evt.getSource() == this.followMouseOverFlag)
+ }
+ else if (evt.getSource() == this.followMouseOverFlag)
{
mouseOverFlag_stateChanged();
}
private void mouseOverFlag_stateChanged()
{
viewport.followHighlight = followMouseOverFlag.getState();
- // TODO: could kick the scrollTo mechanism to reset view for current searchresults.
+ // TODO: could kick the scrollTo mechanism to reset view for current
+ // searchresults.
}
private void centreColumnLabelFlag_stateChanged()
viewport.hideAllSelectedSeqs();
alignPanel.paintAlignment(true);
}
- else if (source == hideAllButSelection) {
- toggleHiddenRegions(false,false);
+ else if (source == hideAllButSelection)
+ {
+ toggleHiddenRegions(false, false);
alignPanel.paintAlignment(true);
}
- else if (source == hideAllSelection) {
+ else if (source == hideAllSelection)
+ {
SequenceGroup sg = viewport.getSelectionGroup();
viewport.expandColSelection(sg, false);
viewport.hideAllSelectedSeqs();
viewport.hideSelectedColumns();
alignPanel.paintAlignment(true);
}
- else if (source == showAllHidden) {
+ else if (source == showAllHidden)
+ {
viewport.showAllHiddenColumns();
viewport.showAllHiddenSeqs();
alignPanel.paintAlignment(true);
{
sortIDMenuItem_actionPerformed();
}
+ else if (source == sortLengthMenuItem)
+ {
+ sortLengthMenuItem_actionPerformed();
+ }
else if (source == sortGroupMenuItem)
{
sortGroupMenuItem_actionPerformed();
private Hashtable getDisplayedFeatureCols()
{
- if (alignPanel.getFeatureRenderer()!=null) {
+ if (alignPanel.getFeatureRenderer() != null)
+ {
FeatureRenderer fr = alignPanel.getFeatureRenderer();
Hashtable fcols = new Hashtable();
Enumeration en = viewport.featuresDisplayed.keys();
while (en.hasMoreElements())
{
Object col = en.nextElement();
- fcols.put(col,fr.featureColours.get(col));
+ fcols.put(col, fr.featureColours.get(col));
}
return fcols;
}
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void undoMenuItem_actionPerformed()
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void redoMenuItem_actionPerformed()
{
this.setVisible(false);
}
}
+
protected void makeGrpsFromSelection_actionPerformed()
{
if (viewport.getSelectionGroup() != null)
for (int g = 0; g < gps.length; g++)
{
// gps[g].setShowunconserved(viewport.getShowUnconserved());
- gps[g].setIncludeAllConsSymbols(viewport.isIncludeAllConsensusSymbols());
+ gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
viewport.alignment.addGroup(gps[g]);
Color col = new Color((int) (Math.random() * 255), (int) (Math
.random() * 255), (int) (Math.random() * 255));
alignPanel.paintAlignment(true);
}
}
+
protected void deleteGroups_actionPerformed()
{
viewport.alignment.deleteAllGroups();
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
}
+
public void invertColSel_actionPerformed()
{
viewport.invertColumnSelection();
* get sequence feature groups that are hidden or shown
*
* @param visible
- * true is visible
+ * true is visible
* @return list
*/
public String[] getFeatureGroupsOfState(boolean visible)
* Change the display state for the given feature groups
*
* @param groups
- * list of group strings
+ * list of group strings
* @param state
- * visible or invisible
+ * visible or invisible
*/
public void setFeatureGroupState(String[] groups, boolean state)
{
modifyPID_actionPerformed();
}
+
public void sortPairwiseMenuItem_actionPerformed()
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
AlignmentSorter.sortByID(viewport.getAlignment());
- addHistoryItem(new OrderCommand("ID Sort", oldOrder,
- viewport.alignment));
+ addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
+ alignPanel.paintAlignment(true);
+ }
+
+ public void sortLengthMenuItem_actionPerformed()
+ {
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+ AlignmentSorter.sortByLength(viewport.getAlignment());
+ addHistoryItem(new OrderCommand("Length Sort", oldOrder, viewport.alignment));
alignPanel.paintAlignment(true);
}
public void PCAMenuItem_actionPerformed()
{
// are the sequences aligned?
- if (!viewport.alignment.isAligned())
+ if (!viewport.alignment.isAligned(false))
{
SequenceI current;
int Width = viewport.getAlignment().getWidth();
void NewTreePanel(String type, String pwType, String title)
{
// are the sequences aligned?
- if (!viewport.alignment.isAligned())
+ if (!viewport.alignment.isAligned(false))
{
SequenceI current;
int Width = viewport.getAlignment().getWidth();
jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
addTreeMenuItem(tp, treeFile);
}
+
/**
* sort the alignment using the given treePanel
- * @param treePanel tree used to sort view
- * @param title string used for undo event name
+ *
+ * @param treePanel
+ * tree used to sort view
+ * @param title
+ * string used for undo event name
*/
public void sortByTree(TreePanel treePanel, String title)
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
- AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel
- .getTree());
+ AlignmentSorter
+ .sortByTree(viewport.getAlignment(), treePanel.getTree());
// addHistoryItem(new HistoryItem("Sort", viewport.alignment,
// HistoryItem.SORT));
- addHistoryItem(new OrderCommand("Order by "+title, oldOrder,
+ addHistoryItem(new OrderCommand("Order by " + title, oldOrder,
viewport.alignment));
alignPanel.paintAlignment(true);
}
+
/**
- * Do any automatic reordering of the alignment and add the necessary bits to the menu structure for the new tree
+ * Do any automatic reordering of the alignment and add the necessary bits to
+ * the menu structure for the new tree
+ *
* @param treePanel
* @param title
*/
- protected void addTreeMenuItem(final TreePanel treePanel, final String title)
+ protected void addTreeMenuItem(final TreePanel treePanel,
+ final String title)
{
final MenuItem item = new MenuItem(title);
sortByTreeMenu.add(item);
class AboutPanel extends Canvas
{
String version;
+
String builddate;
+
public AboutPanel(String version, String builddate)
{
this.version = version;
g.setFont(new Font("Helvetica", Font.BOLD, 14));
g.drawString("JalviewLite - Release " + version, x, y += fh);
g.setFont(new Font("Helvetica", Font.BOLD, 12));
- g.drawString("Build date: "+builddate, x, y += fh);
+ g.drawString("Build date: " + builddate, x, y += fh);
g.setFont(new Font("Helvetica", Font.PLAIN, 12));
g
.drawString(
"For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list",
x, y += fh);
g.drawString("If you use Jalview, please cite:", x, y += fh + 8);
- g.drawString(
- "Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)",x,y+=fh);
- g.drawString("Jalview Version 2 - a multiple sequence alignment editor and analysis workbench",x,y+=fh);
- g.drawString("Bioinformatics doi: 10.1093/bioinformatics/btp033",x,y+=fh);
+ g
+ .drawString(
+ "Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)",
+ x, y += fh);
+ g
+ .drawString(
+ "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench",
+ x, y += fh);
+ g.drawString("Bioinformatics doi: 10.1093/bioinformatics/btp033",
+ x, y += fh);
}
}
Frame frame = new Frame();
- frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite.getBuildDate()));
+ frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
+ .getBuildDate()));
jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 220);
}
{
try
{
- if (url.indexOf(":")==-1)
+ if (url.indexOf(":") == -1)
{
- // TODO: verify (Bas Vroling bug) prepend codebase or server URL to form valid URL
- if (url.indexOf("/")==0)
+ // TODO: verify (Bas Vroling bug) prepend codebase or server URL to
+ // form valid URL
+ if (url.indexOf("/") == 0)
{
String codebase = viewport.applet.getCodeBase().toString();
- url = codebase.substring(0,codebase.length()-viewport.applet.getCodeBase().getFile().length())+url;
- } else {
- url = viewport.applet.getCodeBase()+url;
+ url = codebase.substring(0, codebase.length()
+ - viewport.applet.getCodeBase().getFile().length())
+ + url;
+ }
+ else
+ {
+ url = viewport.applet.getCodeBase() + url;
}
System.out.println("Show url (prepended codebase): " + url);
- } else {
+ }
+ else
+ {
System.out.println("Show url: " + url);
}
viewport.applet.getAppletContext().showDocument(
MenuItem sortIDMenuItem = new MenuItem();
+ MenuItem sortLengthMenuItem = new MenuItem();
+
MenuItem sortGroupMenuItem = new MenuItem();
MenuItem removeRedundancyMenuItem = new MenuItem();
MenuItem deleteGroups = new MenuItem();
- MenuItem grpsFromSelection= new MenuItem();
+ MenuItem grpsFromSelection = new MenuItem();
MenuItem delete = new MenuItem();
sortPairwiseMenuItem.addActionListener(this);
sortIDMenuItem.setLabel("by ID");
sortIDMenuItem.addActionListener(this);
+ sortLengthMenuItem.setLabel("by Length");
+ sortLengthMenuItem.addActionListener(this);
sortGroupMenuItem.setLabel("by Group");
sortGroupMenuItem.addActionListener(this);
removeRedundancyMenuItem.setLabel("Remove Redundancy...");
annotationPanelMenuItem.addItemListener(this);
colourTextMenuItem.setLabel("Colour Text");
colourTextMenuItem.addItemListener(this);
- displayNonconservedMenuItem.setLabel("Show non-conserved");
+ displayNonconservedMenuItem.setLabel("Show nonconserved");
displayNonconservedMenuItem.addItemListener(this);
alProperties.addActionListener(this);
overviewMenuItem.setLabel("Overview Window");
pasteMenu.add(pasteNew);
pasteMenu.add(pasteThis);
sort.add(sortIDMenuItem);
+ sort.add(sortLengthMenuItem);
sort.add(sortByTreeMenu);
sort.add(sortGroupMenuItem);
sort.add(sortPairwiseMenuItem);
selectMenu.add(invertColSel);
selectMenu.add(grpsFromSelection);
selectMenu.add(deleteGroups);
-
+
}
MenuItem featureSettings = new MenuItem();
MenuItem hideSequences = new MenuItem();
MenuItem hideAllButSelection = new MenuItem();
+
MenuItem hideAllSelection = new MenuItem();
+
MenuItem showAllHidden = new MenuItem();
Menu formatMenu = new Menu();
* platform independent manner to avoid OSX/Mac menu appendage daftness.
*
* @param reallyEmbedded
- * true to attach the view to the applet area on the page
- * rather than in a new window
+ * true to attach the view to the applet area on the page rather than
+ * in a new window
*/
public void createAlignFrameWindow(boolean reallyEmbedded, String title)
{
git://source.jalview.org / jalview.git / blobdiff