X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=8ade5d690648ee799b1b4b6c8e31970f63019770;hb=e07868a6fa123b2ff79b7ccc2df7e96485168ec8;hp=dc1f95ba377622a28e0e13b82d237e4a49a7e312;hpb=6168111321deafec25337c6c59210f14f857041d;p=jalview.git
diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index dc1f95b..8ade5d6 100644
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -35,6 +35,7 @@ import jalview.schemes.ResidueProperties;
import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
import jalview.util.Platform;
+import jalview.viewmodel.ViewportRanges;
import java.awt.BorderLayout;
import java.awt.Color;
@@ -69,6 +70,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
{
public AlignViewport av;
+ ViewportRanges vpRanges;
+
OverviewPanel overviewPanel;
private SeqPanel seqPanel;
@@ -91,9 +94,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
// this value is set false when selection area being dragged
boolean fastPaint = true;
- int hextent = 0;
+ private int hextent = 0;
- int vextent = 0;
+ private int vextent = 0;
/*
* Flag set while scrolling to follow complementary cDNA/protein scroll. When
@@ -113,6 +116,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
{
alignFrame = af;
this.av = av;
+ vpRanges = av.getRanges();
setSeqPanel(new SeqPanel(av, this));
setIdPanel(new IdPanel(av, this));
@@ -377,7 +381,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
*/
if (centre)
{
- int offset = (av.getEndRes() - av.getStartRes() + 1) / 2 - 1;
+ int offset = (vpRanges.getEndRes() - vpRanges.getStartRes() + 1) / 2 - 1;
start = Math.max(start - offset, 0);
end = end + offset - 1;
}
@@ -413,7 +417,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
// + av.getStartSeq() + ", ends=" + av.getEndSeq());
if (!av.getWrapAlignment())
{
- if ((startv = av.getStartRes()) >= start)
+ if ((startv = vpRanges.getStartRes()) >= start)
{
/*
* Scroll left to make start of search results visible
@@ -421,7 +425,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
// setScrollValues(start - 1, seqIndex); // plus one residue
setScrollValues(start, seqIndex);
}
- else if ((endv = av.getEndRes()) <= end)
+ else if ((endv = vpRanges.getEndRes()) <= end)
{
/*
* Scroll right to make end of search results visible
@@ -429,19 +433,20 @@ public class AlignmentPanel extends GAlignmentPanel implements
// setScrollValues(startv + 1 + end - endv, seqIndex); // plus one
setScrollValues(startv + end - endv, seqIndex);
}
- else if ((starts = av.getStartSeq()) > seqIndex)
+ else if ((starts = vpRanges.getStartSeq()) > seqIndex)
{
/*
* Scroll up to make start of search results visible
*/
- setScrollValues(av.getStartRes(), seqIndex);
+ setScrollValues(vpRanges.getStartRes(), seqIndex);
}
- else if ((ends = av.getEndSeq()) <= seqIndex)
+ else if ((ends = vpRanges.getEndSeq()) <= seqIndex)
{
/*
* Scroll down to make end of search results visible
*/
- setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1);
+ setScrollValues(vpRanges.getStartRes(), starts + seqIndex - ends
+ + 1);
}
/*
* Else results are already visible - no need to scroll
@@ -464,10 +469,11 @@ public class AlignmentPanel extends GAlignmentPanel implements
{
int cwidth = getSeqPanel().seqCanvas
.getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
- if (res < av.getStartRes() || res >= (av.getStartRes() + cwidth))
+ if (res < vpRanges.getStartRes()
+ || res >= (vpRanges.getStartRes() + cwidth))
{
vscroll.setValue((res / cwidth));
- av.startRes = vscroll.getValue() * cwidth;
+ vpRanges.setStartRes(vscroll.getValue() * cwidth);
}
}
@@ -591,7 +597,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
fontChanged();
setAnnotationVisible(av.isShowAnnotation());
boolean wrap = av.getWrapAlignment();
- av.startSeq = 0;
+ vpRanges.setStartSeq(0);
scalePanelHolder.setVisible(!wrap);
hscroll.setVisible(!wrap);
idwidthAdjuster.setVisible(!wrap);
@@ -688,7 +694,6 @@ public class AlignmentPanel extends GAlignmentPanel implements
*/
public void setScrollValues(int x, int y)
{
- // System.err.println("Scroll " + this.av.viewName + " to " + x + "," + y);
if (av == null || av.getAlignment() == null)
{
return;
@@ -698,12 +703,10 @@ public class AlignmentPanel extends GAlignmentPanel implements
if (av.hasHiddenColumns())
{
+ // reset the width to exclude hidden columns
width = av.getColumnSelection().findColumnPosition(width);
}
- av.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av
- .getCharWidth())) - 1);
-
hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
vextent = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight();
@@ -737,6 +740,10 @@ public class AlignmentPanel extends GAlignmentPanel implements
x = 0;
}
+ // update endRes after x has (possibly) been adjusted
+ vpRanges.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av
+ .getCharWidth())) - 1);
+
/*
* each scroll adjustment triggers adjustmentValueChanged, which resets the
* 'do not scroll complement' flag; ensure it is the same for both
@@ -757,14 +764,14 @@ public class AlignmentPanel extends GAlignmentPanel implements
@Override
public void adjustmentValueChanged(AdjustmentEvent evt)
{
- int oldX = av.getStartRes();
- int oldY = av.getStartSeq();
+ int oldX = vpRanges.getStartRes();
+ int oldY = vpRanges.getStartSeq();
if (evt.getSource() == hscroll)
{
int x = hscroll.getValue();
- av.setStartRes(x);
- av.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av
+ vpRanges.setStartRes(x);
+ vpRanges.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av
.getCharWidth())) - 1);
}
@@ -778,8 +785,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
{
int rowSize = getSeqPanel().seqCanvas
.getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
- av.setStartRes(offy * rowSize);
- av.setEndRes((offy + 1) * rowSize);
+ vpRanges.setStartRes(offy * rowSize);
+ vpRanges.setEndRes((offy + 1) * rowSize);
}
else
{
@@ -791,16 +798,18 @@ public class AlignmentPanel extends GAlignmentPanel implements
@Override
public void run()
{
- setScrollValues(av.getStartRes(), av.getStartSeq());
+ setScrollValues(vpRanges.getStartRes(),
+ vpRanges.getStartSeq());
}
});
}
}
else
{
- av.setStartSeq(offy);
- av.setEndSeq(offy
- + (getSeqPanel().seqCanvas.getHeight() / av.getCharHeight()));
+ vpRanges.setStartSeq(offy);
+ vpRanges.setEndSeq(offy
+ + (getSeqPanel().seqCanvas.getHeight() / av.getCharHeight())
+ - 1);
}
}
@@ -809,8 +818,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
overviewPanel.setBoxPosition();
}
- int scrollX = av.startRes - oldX;
- int scrollY = av.startSeq - oldY;
+ int scrollX = vpRanges.getStartRes() - oldX;
+ int scrollY = vpRanges.getStartSeq() - oldY;
if (av.getWrapAlignment() || !fastPaint)
{
@@ -820,13 +829,13 @@ public class AlignmentPanel extends GAlignmentPanel implements
{
// Make sure we're not trying to draw a panel
// larger than the visible window
- if (scrollX > av.endRes - av.startRes)
+ if (scrollX > vpRanges.getEndRes() - vpRanges.getStartRes())
{
- scrollX = av.endRes - av.startRes;
+ scrollX = vpRanges.getEndRes() - vpRanges.getStartRes();
}
- else if (scrollX < av.startRes - av.endRes)
+ else if (scrollX < vpRanges.getStartRes() - vpRanges.getEndRes())
{
- scrollX = av.startRes - av.endRes;
+ scrollX = vpRanges.getStartRes() - vpRanges.getEndRes();
}
if (scrollX != 0 || scrollY != 0)
@@ -926,7 +935,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
}
else
{
- setScrollValues(av.getStartRes(), av.getStartSeq());
+ setScrollValues(vpRanges.getStartRes(), vpRanges.getStartSeq());
}
}
@@ -1299,8 +1308,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
if (onscreen
|| (idwidth = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH")) == null)
{
- return (getIdPanel().getWidth() > 0 ? getIdPanel().getWidth()
- : calculateIdWidth().width + 4);
+ int w = getIdPanel().getWidth();
+ return (w > 0 ? w : calculateIdWidth().width + 4);
}
return idwidth.intValue() + 4;
}
@@ -1448,7 +1457,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
public void makePNGImageMap(File imgMapFile, String imageName)
{
- // /////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS
+ // /////ONLY WORKS WITH NON WRAPPED ALIGNMENTS
// ////////////////////////////////////////////
int idWidth = getVisibleIdWidth(false);
FontMetrics fm = getFontMetrics(av.getFont());
@@ -1462,7 +1471,6 @@ public class AlignmentPanel extends GAlignmentPanel implements
{
int s, sSize = av.getAlignment().getHeight(), res, alwidth = av
.getAlignment().getWidth(), g, gSize, f, fSize, sy;
- StringBuffer text = new StringBuffer();
PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
out.println(jalview.io.HTMLOutput.getImageMapHTML());
out.println(" res)
{
- text.append("
" + groups[g].getName() + "");
+ text.append("
").append(groups[g].getName())
+ .append("");
}
}
@@ -1521,12 +1531,13 @@ public class AlignmentPanel extends GAlignmentPanel implements
{
if (text.length() < 1)
{
- text.append("= seq.findPosition(res)))
{
- if (features[f].getType().equals("disulfide bond"))
+ if (features[f].isContactFeature())
{
if (features[f].getBegin() == seq.findPosition(res)
|| features[f].getEnd() == seq
.findPosition(res))
{
- text.append("
disulfide bond "
- + features[f].getBegin() + ":"
- + features[f].getEnd());
+ text.append("
").append(features[f].getType())
+ .append(" ").append(features[f].getBegin())
+ .append(":").append(features[f].getEnd());
}
}
else
@@ -1554,13 +1565,13 @@ public class AlignmentPanel extends GAlignmentPanel implements
&& !features[f].getType().equals(
features[f].getDescription()))
{
- text.append(" " + features[f].getDescription());
+ text.append(" ").append(features[f].getDescription());
}
if (features[f].getValue("status") != null)
{
- text.append(" (" + features[f].getValue("status")
- + ")");
+ text.append(" (").append(features[f].getValue("status"))
+ .append(")");
}
}
}
@@ -1873,4 +1884,26 @@ public class AlignmentPanel extends GAlignmentPanel implements
{
return this.dontScrollComplement;
}
+
+ /**
+ * Redraw sensibly.
+ *
+ * @adjustHeight if true, try to recalculate panel height for visible
+ * annotations
+ */
+ protected void refresh(boolean adjustHeight)
+ {
+ validateAnnotationDimensions(adjustHeight);
+ addNotify();
+ if (adjustHeight)
+ {
+ // sort, repaint, update overview
+ paintAlignment(true);
+ }
+ else
+ {
+ // lightweight repaint
+ repaint();
+ }
+ }
}