/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* 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.
- *
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
* 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/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
-import java.awt.*;
-import java.awt.event.*;
-import java.util.Hashtable;
-import java.util.Vector;
-
import jalview.api.AlignmentViewPanel;
-import jalview.datamodel.*;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SequenceI;
import jalview.structure.StructureSelectionManager;
-public class AlignmentPanel extends Panel implements AdjustmentListener, AlignmentViewPanel
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.FontMetrics;
+import java.awt.Frame;
+import java.awt.Graphics;
+import java.awt.Panel;
+import java.awt.Scrollbar;
+import java.awt.event.AdjustmentEvent;
+import java.awt.event.AdjustmentListener;
+import java.awt.event.ComponentAdapter;
+import java.awt.event.ComponentEvent;
+
+public class AlignmentPanel extends Panel implements AdjustmentListener,
+ AlignmentViewPanel
{
public AlignViewport av;
// this value is set false when selection area being dragged
boolean fastPaint = true;
-
- public void finalize() {
- alignFrame=null;
- av=null;
- seqPanel=null;
- seqPanelHolder=null;
- sequenceHolderPanel=null;
- scalePanel=null;
- scalePanelHolder=null;
- annotationPanel=null;
- annotationPanelHolder=null;
- annotationSpaceFillerHolder=null;
+
+ public void finalize()
+ {
+ alignFrame = null;
+ av = null;
+ seqPanel = null;
+ seqPanelHolder = null;
+ sequenceHolderPanel = null;
+ scalePanel = null;
+ scalePanelHolder = null;
+ annotationPanel = null;
+ annotationPanelHolder = null;
+ annotationSpaceFillerHolder = null;
}
+
public AlignmentPanel(AlignFrame af, final AlignViewport av)
{
try
annotationPanelHolder.add(annotationPanel, BorderLayout.CENTER);
sequenceHolderPanel.add(annotationPanelHolder, BorderLayout.SOUTH);
-
alabels = new AnnotationLabels(this);
setAnnotationVisible(av.showAnnotation);
public void componentResized(ComponentEvent evt)
{
setScrollValues(av.getStartRes(), av.getStartSeq());
- if (getSize().height>0 && annotationPanelHolder.getSize().height>0) {
+ if (getSize().height > 0
+ && annotationPanelHolder.getSize().height > 0)
+ {
validateAnnotationDimensions(false);
}
repaint();
}
-
+
});
Dimension d = calculateIdWidth();
}
}
});
-
}
public SequenceRenderer getSequenceRenderer()
Dimension d = calculateIdWidth();
d.setSize(d.width + 4, seqPanel.seqCanvas.getSize().height);
alabels.setSize(d.width + 4, ap);
-
+
idPanel.idCanvas.setSize(d);
hscrollFillerPanel.setSize(d);
-
+
validateAnnotationDimensions(false);
annotationPanel.repaint();
validate();
{
idPanel.idCanvas.setSize(w, h);
idPanelHolder.setSize(w, idPanelHolder.getSize().height);
- annotationSpaceFillerHolder.setSize(w,annotationSpaceFillerHolder.getSize().height);
+ annotationSpaceFillerHolder.setSize(w,
+ annotationSpaceFillerHolder.getSize().height);
alabels.setSize(w, alabels.getSize().height);
validate();
}
public boolean scrollToPosition(SearchResults results,
boolean redrawOverview)
{
-
+
// do we need to scroll the panel?
if (results != null && results.getSize() > 0)
{
- int seqIndex = av.alignment.findIndex(results);
+ AlignmentI alignment = av.getAlignment();
+ int seqIndex = alignment.findIndex(results);
if (seqIndex == -1)
{
return false;
}
- SequenceI seq = av.alignment.getSequenceAt(seqIndex);
- int[] r = results.getResults(seq, 0,av.alignment.getWidth());
+ SequenceI seq = alignment.getSequenceAt(seqIndex);
+ int[] r = results.getResults(seq, 0, alignment.getWidth());
if (r == null)
{
- if (av.applet.debug) {// DEBUG
- System.out.println("DEBUG: scroll didn't happen - results not within alignment : "+seq.getStart()+","+seq.getEnd());
+ if (av.applet.debug)
+ {// DEBUG
+ System.out
+ .println("DEBUG: scroll didn't happen - results not within alignment : "
+ + seq.getStart() + "," + seq.getEnd());
}
return false;
}
- if (av.applet.debug) {
+ if (av.applet.debug)
+ {
// DEBUG
- /*System.out.println("DEBUG: scroll: start=" + r[0]
- + " av.getStartRes()=" + av.getStartRes() + " end=" + r[1]
- + " seq.end=" + seq.getEnd() + " av.getEndRes()="
- + av.getEndRes() + " hextent=" + hextent);
+ /*
+ * System.out.println("DEBUG: scroll: start=" + r[0] +
+ * " av.getStartRes()=" + av.getStartRes() + " end=" + r[1] +
+ * " seq.end=" + seq.getEnd() + " av.getEndRes()=" + av.getEndRes() +
+ * " hextent=" + hextent);
*/
}
int start = r[0];
}
return true;
}
- public boolean scrollTo(int ostart, int end, int seqIndex, boolean scrollToNearest, boolean redrawOverview)
+
+ public boolean scrollTo(int ostart, int end, int seqIndex,
+ boolean scrollToNearest, boolean redrawOverview)
{
- int startv, endv, starts, ends, width;
+ int startv, endv, starts, ends, width;
- int start=-1;
- if (av.hasHiddenColumns)
+ int start = -1;
+ if (av.hasHiddenColumns())
{
start = av.getColumnSelection().findColumnPosition(ostart);
end = av.getColumnSelection().findColumnPosition(end);
if (start == end)
{
- if (!scrollToNearest && !av.colSel.isVisible(ostart))
+ if (!scrollToNearest && !av.getColumnSelection().isVisible(ostart))
{
// don't scroll - position isn't visible
return false;
}
if (!av.wrapAlignment)
{
- /*
- int spos=av.getStartRes(),sqpos=av.getStartSeq();
- if ((startv = av.getStartRes()) >= start)
- {
- spos=start-1;
-// seqIn
-// setScrollValues(start - 1, seqIndex);
- }
- else if ((endv = av.getEndRes()) <= end)
- {
-// setScrollValues(spos=startv + 1 + end - endv, seqIndex);
- spos=startv + 1 + end - endv;
- }
- else if ((starts = av.getStartSeq()) > seqIndex)
- {
- setScrollValues(av.getStartRes(), seqIndex);
- }
- else if ((ends = av.getEndSeq()) <= seqIndex)
+ /*
+ * int spos=av.getStartRes(),sqpos=av.getStartSeq(); if ((startv =
+ * av.getStartRes()) >= start) { spos=start-1; // seqIn //
+ * setScrollValues(start - 1, seqIndex); } else if ((endv =
+ * av.getEndRes()) <= end) { // setScrollValues(spos=startv + 1 + end -
+ * endv, seqIndex); spos=startv + 1 + end - endv; } else if ((starts =
+ * av.getStartSeq()) > seqIndex) { setScrollValues(av.getStartRes(),
+ * seqIndex); } else if ((ends = av.getEndSeq()) <= seqIndex) {
+ * setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1); }
+ *
+ * /*
+ */
+ if ((av.getStartRes() > end)
+ || (av.getEndRes() < start)
+ || ((av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))
+ {
+ if (start > av.getAlignment().getWidth() - hextent)
+ {
+ start = av.getAlignment().getWidth() - hextent;
+ if (start < 0)
{
- setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1);
+ start = 0;
}
- /* */
- if ((av.getStartRes() > end)
- || (av.getEndRes() < start)
- || ((av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))
+ }
+ if (seqIndex > av.getAlignment().getHeight() - vextent)
{
- if (start > av.alignment.getWidth() - hextent)
- {
- start = av.alignment.getWidth() - hextent;
- if (start < 0)
- {
- start = 0;
- }
-
- }
- if (seqIndex > av.alignment.getHeight() - vextent)
+ seqIndex = av.getAlignment().getHeight() - vextent;
+ if (seqIndex < 0)
{
- seqIndex = av.alignment.getHeight() - vextent;
- if (seqIndex < 0)
- {
- seqIndex = 0;
- }
+ seqIndex = 0;
}
- // System.out.println("trying to scroll to: "+start+" "+seqIndex);
- setScrollValues(start, seqIndex);
- }/**/
- }
- else
- {
- scrollToWrappedVisible(start);
- }
+ }
+ // System.out.println("trying to scroll to: "+start+" "+seqIndex);
+ setScrollValues(start, seqIndex);
+ }/**/
+ }
+ else
+ {
+ scrollToWrappedVisible(start);
+ }
if (redrawOverview && overviewPanel != null)
{
overviewPanel.setBoxPosition();
annotationSpaceFillerHolder.setVisible(b);
annotationPanelHolder.setVisible(b);
}
+ else
+ {
+ annotationSpaceFillerHolder.setVisible(false);
+ annotationPanelHolder.setVisible(false);
+ }
validate();
repaint();
}
-
+
/**
* automatically adjust annotation panel height for new annotation whilst
* ensuring the alignment is still visible.
validate();
paintAlignment(true);
}
+
/**
* calculate the annotation dimensions and refresh slider values accordingly.
- * need to do repaints/notifys afterwards.
+ * need to do repaints/notifys afterwards.
*/
- protected void validateAnnotationDimensions(boolean adjustPanelHeight) {
- boolean modified=false;
- int height = annotationPanel.calcPanelHeight();
- int minsize=0;
+ protected void validateAnnotationDimensions(boolean adjustPanelHeight)
+ {
+ boolean modified = false;
+ int height = av.calcPanelHeight();
+ int minsize = 0;
if (hscroll.isVisible())
{
- height += (minsize=hscroll.getPreferredSize().height);
+ height += (minsize = hscroll.getPreferredSize().height);
}
- if (apvscroll.isVisible()) {
- minsize+=apvscroll.getPreferredSize().height;
+ if (apvscroll.isVisible())
+ {
+ minsize += apvscroll.getPreferredSize().height;
}
int mheight = height;
- Dimension d=sequenceHolderPanel.getSize(),e=idPanel.getSize();
- int seqandannot=d.height-scalePanelHolder.getSize().height;
- // sets initial preferred height
- if ((height+40) > seqandannot / 2)
- {
- height = seqandannot / 2;
+ Dimension d = sequenceHolderPanel.getSize(), e = idPanel.getSize();
+ int seqandannot = d.height - scalePanelHolder.getSize().height;
+
+ if (adjustPanelHeight)
+ {
+ // NOTE: this logic is different in the application. Need a better
+ // algorithm to define behaviour
+ // sets initial preferred height
+ // try and set height according to alignment
+ float sscaling = (float) ((av.getCharHeight() * av.getAlignment()
+ .getHeight()) / (1.0 * mheight));
+ if (sscaling > 0.5)
+ {
+ // if the alignment is too big then
+ // default is 0.5 split
+ height = seqandannot / 2;
+ }
+ else
+ {
+ // otherwise just set the panel so that one row of sequence is visible
+ height = -av.getCharHeight() * 1
+ + (int) (seqandannot * (1 - sscaling));
+ }
}
- if (!adjustPanelHeight)
+ else
{
// maintain same window layout whilst updating sliders
- height=annotationPanelHolder.getSize().height;
+ height = annotationPanelHolder.getSize().height;
}
-
- if (seqandannot-height<5)
+
+ if (seqandannot - height < 5)
{
height = seqandannot;
}
- annotationPanel.setSize(new Dimension(d.width,height));
- alabels.setSize(new Dimension(e.width,height));
+ annotationPanel.setSize(new Dimension(d.width, height));
+ alabels.setSize(new Dimension(e.width, height));
annotationSpaceFillerHolder.setSize(new Dimension(e.width, height));
annotationPanelHolder.setSize(new Dimension(d.width, height));
- seqPanelHolder.setSize(d.width,seqandannot-height);
- seqPanel.seqCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
- int s=apvscroll.getValue();
- if (s>mheight-height)
+ // seqPanelHolder.setSize(d.width, seqandannot - height);
+ seqPanel.seqCanvas
+ .setSize(d.width, seqPanel.seqCanvas.getSize().height);
+ int s = apvscroll.getValue();
+ if (s > mheight - height)
{
s = 0;
}
apvscroll.setValues(s, height, 0, mheight);
- annotationPanel.setScrollOffset(apvscroll.getValue());
- alabels.setScrollOffset(apvscroll.getValue());
+ annotationPanel.setScrollOffset(apvscroll.getValue(), false);
+ alabels.setScrollOffset(apvscroll.getValue(), false);
}
-
+
public void setWrapAlignment(boolean wrap)
{
av.startSeq = 0;
fontChanged(); // This is so that the scalePanel is resized correctly
validate();
+ sequenceHolderPanel.validate();
repaint();
}
public void setScrollValues(int x, int y)
{
- int width = av.alignment.getWidth();
- int height = av.alignment.getHeight();
+ int width = av.getAlignment().getWidth();
+ int height = av.getAlignment().getHeight();
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
width = av.getColumnSelection().findColumnPosition(width);
}
- if (x<0) { x = 0; };
+ if (x < 0)
+ {
+ x = 0;
+ }
+ ;
hextent = seqPanel.seqCanvas.getSize().width / av.charWidth;
vextent = seqPanel.seqCanvas.getSize().height / av.charHeight;
-
+
if (hextent > width)
{
hextent = width;
if ((hextent + x) > width)
{
- System.err.println("hextent was "+hextent+" and x was "+x);
+ System.err.println("hextent was " + hextent + " and x was " + x);
x = width - hextent;
}
if (x < 0)
{
- System.err.println("x was "+x);
+ System.err.println("x was " + x);
x = 0;
}
av.setStartSeq(y);
int endSeq = y + vextent;
- if (endSeq > av.alignment.getHeight())
+ if (endSeq > av.getAlignment().getHeight())
{
- endSeq = av.alignment.getHeight();
+ endSeq = av.getAlignment().getHeight();
}
av.setEndSeq(endSeq);
}
sendViewPosition();
-
}
public void adjustmentValueChanged(AdjustmentEvent evt)
if (evt == null || evt.getSource() == apvscroll)
{
- annotationPanel.setScrollOffset(apvscroll.getValue());
- alabels.setScrollOffset(apvscroll.getValue());
+ annotationPanel.setScrollOffset(apvscroll.getValue(), false);
+ alabels.setScrollOffset(apvscroll.getValue(), false);
// annotationPanel.image=null;
// alabels.image=null;
// alabels.repaint();
sendViewPosition();
}
+
private void sendViewPosition()
{
- StructureSelectionManager.getStructureSelectionManager(av.applet).sendViewPosition(this, av.startRes, av.endRes, av.startSeq, av.endSeq);
+ StructureSelectionManager.getStructureSelectionManager(av.applet)
+ .sendViewPosition(this, av.startRes, av.endRes, av.startSeq,
+ av.endSeq);
}
public void paintAlignment(boolean updateOverview)
if (updateOverview)
{
jalview.structure.StructureSelectionManager
- .getStructureSelectionManager(av.applet).sequenceColoursChanged(this);
+ .getStructureSelectionManager(av.applet)
+ .sequenceColoursChanged(this);
if (overviewPanel != null)
{
invalidate();
Dimension d = idPanel.idCanvas.getSize();
idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
-
+
if (av.getWrapAlignment())
{
- int maxwidth = av.alignment.getWidth();
+ int maxwidth = av.getAlignment().getWidth();
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
}
setScrollValues(av.getStartRes(), av.getStartSeq());
}
- alabels.repaint();
-
seqPanel.seqCanvas.repaint();
- scalePanel.repaint();
- annotationPanel.repaint();
idPanel.idCanvas.repaint();
+ if (!av.wrapAlignment)
+ {
+ if (av.showAnnotation)
+ {
+ alabels.repaint();
+ annotationPanel.repaint();
+ }
+ scalePanel.repaint();
+ }
+
}
protected Panel sequenceHolderPanel = new Panel();
// idPanelHolder.setPreferredSize(new Dimension(70, 10));
this.setLayout(borderLayout7);
- //sequenceHolderPanel.setPreferredSize(new Dimension(150, 150));
+ // sequenceHolderPanel.setPreferredSize(new Dimension(150, 150));
sequenceHolderPanel.setLayout(borderLayout3);
seqPanelHolder.setLayout(borderLayout1);
scalePanelHolder.setBackground(Color.white);
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
+ updateAnnotation(applyGlobalSettings, false);
+ }
- 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();
+ public void updateAnnotation(boolean applyGlobalSettings,
+ boolean preserveNewGroupSettings)
+ {
+ av.updateGroupAnnotationSettings(applyGlobalSettings,
+ preserveNewGroupSettings);
adjustAnnotationHeight();
}
@Override
public AlignmentI getAlignment()
{
- return av.alignment;
+ return av.getAlignment();
}
+
+ @Override
+ public String getViewName()
+ {
+ return getName();
+ }
+
@Override
public StructureSelectionManager getStructureSelectionManager()
{
- return StructureSelectionManager.getStructureSelectionManager(av.applet);
+ return StructureSelectionManager
+ .getStructureSelectionManager(av.applet);
}
+
@Override
public void raiseOOMWarning(String string, OutOfMemoryError error)
{
// TODO: JAL-960
- System.err.println("Out of memory whilst '"+string+"'");
+ System.err.println("Out of memory whilst '" + string + "'");
error.printStackTrace();
}
git://source.jalview.org / jalview.git / blobdiff