/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * 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.gui;
import java.beans.*;
import java.io.*;
+import java.util.Hashtable;
+import java.util.Vector;
import java.awt.*;
import java.awt.event.*;
import java.awt.print.*;
import javax.swing.*;
+import jalview.bin.Cache;
import jalview.datamodel.*;
import jalview.jbgui.*;
import jalview.schemes.*;
* Creates a new AlignmentPanel object.
*
* @param af
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param av
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public AlignmentPanel(AlignFrame af, final AlignViewport av)
{
AlignmentI al = av.getAlignment();
int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300);
- int maxwidth = Math.max(20, Math.min(afwidth - 200, (int) 2 * afwidth
- / 3));
+ int maxwidth = Math.max(20,
+ Math.min(afwidth - 200, (int) 2 * afwidth / 3));
int i = 0;
int idWidth = 0;
String id;
* DOCUMENT ME!
*
* @param results
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void highlightSearchResults(SearchResults results)
{
scrollToPosition(results);
seqPanel.seqCanvas.highlightSearchResults(results);
}
+
/**
- * scroll the view to show the position of the highlighted
- * region in results (if any) and redraw the overview
+ * scroll the view to show the position of the highlighted region in results
+ * (if any) and redraw the overview
+ *
* @param results
*/
- public boolean scrollToPosition(SearchResults results) {
+ public boolean scrollToPosition(SearchResults results)
+ {
return scrollToPosition(results, true);
}
+
/**
- * scroll the view to show the position of the highlighted
- * region in results (if any)
+ * scroll the view to show the position of the highlighted region in results
+ * (if any)
+ *
* @param results
- * @param redrawOverview - when set, the overview will be recalculated (takes longer)
+ * @param redrawOverview
+ * - when set, the overview will be recalculated (takes longer)
* @return false if results were not found
*/
- public boolean scrollToPosition(SearchResults results, boolean redrawOverview) {
- // TODO: properly locate search results in view when large numbers of hidden columns exist before highlighted region
+ public boolean scrollToPosition(SearchResults results,
+ boolean redrawOverview)
+ {
+ int startv, endv, starts, ends, width;
+ // TODO: properly locate search results in view when large numbers of hidden
+ // columns exist before highlighted region
// do we need to scroll the panel?
- if (results != null && results.getSize()>0)
+ // TODO: tons of nullpointereexceptions raised here.
+ if (results != null && results.getSize() > 0 && av != null
+ && av.alignment != null)
{
int seqIndex = av.alignment.findIndex(results);
- if (seqIndex==-1)
+ if (seqIndex == -1)
{
return false;
}
SequenceI seq = av.alignment.getSequenceAt(seqIndex);
-
- int [] r = results.getResults(seq, seq.getStart(), seq.getEnd());
- if (r==null)
+
+ int[] r = results.getResults(seq, 0, av.alignment.getWidth()); // results.getResults(seq,
+ // seq.getStart(),
+ // seq.getEnd());
+ // TODO: VAMSAS: fix hidden column issue where scroll to left from C
+ // terminus is not visible
+ if (r == null)
{
return false;
}
int start = r[0];
int end = r[1];
- if (start<0)
+ // System.err.println("Seq : "+seqIndex+" Scroll to "+start+","+end); //
+ // DEBUG
+ if (start < 0)
{
return false;
}
- if (end==seq.getEnd())
+ if (end == seq.getEnd())
{
return false;
}
if (!av.wrapAlignment)
{
- if ((av.getStartRes() >= start)
- || (av.getEndRes() <= end))
+ if ((startv = av.getStartRes()) >= start)
{
- setScrollValues(start-1, seqIndex);
- } else if ((av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex))
+ setScrollValues(start - 1, seqIndex);
+ }
+ else if ((endv = av.getEndRes()) <= end)
+ {
+ setScrollValues(startv + 1 + end - endv, seqIndex);
+ }
+ else if ((starts = av.getStartSeq()) > seqIndex)
{
setScrollValues(av.getStartRes(), seqIndex);
}
+ else if ((ends = av.getEndSeq()) <= seqIndex)
+ {
+ setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1);
+ }
}
else
{
scrollToWrappedVisible(start);
}
}
- if (!redrawOverview && overviewPanel!=null)
+ if (!redrawOverview && overviewPanel != null)
{
overviewPanel.setBoxPosition();
- }
+ }
paintAlignment(!redrawOverview);
return true;
}
{
int cwidth = seqPanel.seqCanvas
.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
- if (res < av.getStartRes() || res >= (av.getStartRes()+cwidth))
+ if (res < av.getStartRes() || res >= (av.getStartRes() + cwidth))
{
vscroll.setValue((res / cwidth));
av.startRes = vscroll.getValue() * cwidth;
* DOCUMENT ME!
*
* @param op
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setOverviewPanel(OverviewPanel op)
{
* DOCUMENT ME!
*
* @param b
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setAnnotationVisible(boolean b)
{
annotationSpaceFillerHolder.setPreferredSize(new Dimension(
annotationSpaceFillerHolder.getWidth(), height));
annotationScroller.validate();// repaint();
+ addNotify();
repaint();
}
* DOCUMENT ME!
*
* @param wrap
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setWrapAlignment(boolean wrap)
{
* DOCUMENT ME!
*
* @param right
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
* DOCUMENT ME!
*
* @param x
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param y
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setScrollValues(int x, int y)
{
- if (av==null || av.alignment==null)
+ // System.err.println("Scroll to "+x+","+y);
+ if (av == null || av.alignment == null)
{
return;
}
* DOCUMENT ME!
*
* @param evt
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void adjustmentValueChanged(AdjustmentEvent evt)
{
{
int x = hscroll.getValue();
av.setStartRes(x);
- av
- .setEndRes((x + (seqPanel.seqCanvas.getWidth() / av
- .getCharWidth())) - 1);
+ av.setEndRes((x + (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) - 1);
}
if (evt.getSource() == vscroll)
* DOCUMENT ME!
*
* @param g
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void paintComponent(Graphics g)
{
* DOCUMENT ME!
*
* @param pg
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param pf
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param pi
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @return DOCUMENT ME!
*
* @throws PrinterException
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public int print(Graphics pg, PageFormat pf, int pi)
throws PrinterException
* DOCUMENT ME!
*
* @param pg
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param pwidth
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param pheight
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param pi
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @return DOCUMENT ME!
*
* @throws PrinterException
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi)
throws PrinterException
}
pg.setColor(currentColor);
- pg.fillRect(0, (i - startSeq) * av.charHeight, idWidth, av
- .getCharHeight());
+ pg.fillRect(0, (i - startSeq) * av.charHeight, idWidth,
+ av.getCharHeight());
pg.setColor(currentTextColor);
- 4;
}
- pg.drawString(seq.getDisplayId(av.getShowJVSuffix()), xPos,
+ pg.drawString(
+ seq.getDisplayId(av.getShowJVSuffix()),
+ xPos,
(((i - startSeq) * av.charHeight) + av.getCharHeight())
- (av.getCharHeight() / 5));
}
* DOCUMENT ME!
*
* @param pg
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param pwidth
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param pheight
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param pi
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @return DOCUMENT ME!
*
* @throws PrinterException
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public int printWrappedAlignment(Graphics pg, int pwidth, int pheight,
int pi) throws PrinterException
return height;
}
+
+ /**
+ * close the panel - deregisters all listeners and nulls any references to
+ * alignment data.
+ */
+ public void closePanel()
+ {
+ jalview.structure.StructureSelectionManager ssm = jalview.structure.StructureSelectionManager
+ .getStructureSelectionManager();
+ ssm.removeStructureViewerListener(seqPanel, null);
+ ssm.removeSelectionListener(seqPanel);
+ PaintRefresher.RemoveComponent(seqPanel.seqCanvas);
+ PaintRefresher.RemoveComponent(idPanel.idCanvas);
+ PaintRefresher.RemoveComponent(this);
+ if (av != null)
+ {
+ av.alignment = null;
+ av = null;
+ }
+ else
+ {
+ if (Cache.log.isDebugEnabled())
+ {
+ Cache.log.warn("Closing alignment panel which is already closed.");
+ }
+ }
+ }
+
+ /**
+ * hides or shows dynamic annotation rows based on groups and av state flags
+ */
+ public void updateAnnotation()
+ {
+ updateAnnotation(false);
+ }
+
+ public void updateAnnotation(boolean applyGlobalSettings)
+ {
+ // TODO: this should be merged with other annotation update stuff - that
+ // sits on AlignViewport
+ boolean updateCalcs = false;
+ boolean conv = av.isShowGroupConservation();
+ boolean cons = av.isShowGroupConsensus();
+ boolean showprf = av.isShowSequenceLogo();
+ boolean showConsHist = av.isShowConsensusHistogram();
+
+ boolean sortg = true;
+
+ // remove old automatic annotation
+ // add any new annotation
+
+ Vector gr = av.alignment.getGroups(); // OrderedBy(av.alignment.getSequencesArray());
+ // intersect alignment annotation with alignment groups
+
+ AlignmentAnnotation[] aan = av.alignment.getAlignmentAnnotation();
+ Hashtable oldrfs = new Hashtable();
+ if (aan != null)
+ {
+ for (int an = 0; an < aan.length; an++)
+ {
+ if (aan[an].autoCalculated && aan[an].groupRef != null)
+ {
+ oldrfs.put(aan[an].groupRef, aan[an].groupRef);
+ av.alignment.deleteAnnotation(aan[an]);
+ aan[an] = null;
+ }
+ }
+ }
+ SequenceGroup sg;
+ if (gr != null)
+ {
+ for (int g = 0; g < gr.size(); g++)
+ {
+ updateCalcs = false;
+ sg = (SequenceGroup) gr.elementAt(g);
+ if (applyGlobalSettings || !oldrfs.containsKey(sg))
+ {
+ // set defaults for this group's conservation/consensus
+ sg.setshowSequenceLogo(showprf);
+ sg.setShowConsensusHistogram(showConsHist);
+ }
+ if (conv)
+ {
+ updateCalcs = true;
+ av.alignment.addAnnotation(sg.getConservationRow(), 0);
+ }
+ if (cons)
+ {
+ updateCalcs = true;
+ av.alignment.addAnnotation(sg.getConsensus(), 0);
+ }
+ // refresh the annotation rows
+ if (updateCalcs)
+ {
+ sg.recalcConservation();
+ }
+ }
+ }
+ oldrfs.clear();
+ adjustAnnotationHeight();
+ }
}
git://source.jalview.org / jalview.git / blobdiff