X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=f1a8af7f4eab439f57b57e748c03748f81e3f16c;hb=4b7d3640209c4434d569c746672cf9eed4250ace;hp=4f5b7d04ec17d18ee171ca8dc2de561fb1728ea1;hpb=2afaba8da802954edbedf5c0748412d965763a2c;p=jalview.git
diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 4f5b7d0..f1a8af7 100755
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -41,6 +41,7 @@ import java.awt.event.MouseWheelListener;
import java.awt.image.BufferedImage;
import java.beans.PropertyChangeEvent;
import java.util.ArrayList;
+import java.util.BitSet;
import java.util.Collections;
import java.util.List;
@@ -56,7 +57,9 @@ import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.ContactListI;
+import jalview.datamodel.ContactMatrixI;
import jalview.datamodel.ContactRange;
+import jalview.datamodel.GraphLine;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.SequenceI;
import jalview.gui.JalviewColourChooser.ColourChooserListener;
@@ -69,6 +72,7 @@ import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.viewmodel.ViewportListenerI;
import jalview.viewmodel.ViewportRanges;
+import jalview.ws.datamodel.alphafold.PAEContactMatrix;
/**
* AnnotationPanel displays visible portion of annotation rows below unwrapped
@@ -150,6 +154,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
private MouseWheelListener[] _mwl;
+ private boolean notJustOne;
+
/**
* Creates a new AnnotationPanel object.
*
@@ -586,41 +592,166 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
if (graphStretch != -1)
{
- if (aa[graphStretch].graph == AlignmentAnnotation.CUSTOMRENDERER)
+ if (aa[graphStretch].graph == AlignmentAnnotation.CONTACT_MAP)
{
+ // data in row has position on y as well as x axis
if (evt.isAltDown() || evt.isAltGraphDown())
{
dragMode = DragMode.MatrixSelect;
firstDragX = mouseDragLastX;
firstDragY = mouseDragLastY;
}
- else
+ }
+ }
+ else
+ {
+ // no row (or row that can be adjusted) was pressed. Simulate a ruler
+ // click
+ ap.getScalePanel().mousePressed(evt);
+ }
+ }
+
+ /**
+ * checks whether the annotation row under the mouse click evt's handles the
+ * event
+ *
+ * @param evt
+ * @return false if evt was not handled
+ */
+ boolean matrix_clicked(MouseEvent evt)
+ {
+ int[] rowIndex = getRowIndexAndOffset(evt.getY(),
+ av.getAlignment().getAlignmentAnnotation());
+ if (rowIndex == null)
+ {
+ jalview.bin.Console
+ .error("IMPLEMENTATION ERROR: matrix click out of range.");
+ return false;
+ }
+ int yOffset = rowIndex[1];
+
+ AlignmentAnnotation clicked = av.getAlignment()
+ .getAlignmentAnnotation()[rowIndex[0]];
+ if (clicked.graph != AlignmentAnnotation.CONTACT_MAP)
+ {
+ return false;
+ }
+
+ // TODO - use existing threshold to select related sections of matrix
+ GraphLine thr = clicked.getThreshold();
+
+ int currentX = getColumnForXPos(evt.getX());
+ ContactListI forCurrentX = av.getContactList(clicked, currentX);
+ if (forCurrentX != null)
+ {
+ ContactGeometry cXcgeom = new ContactGeometry(forCurrentX,
+ clicked.graphHeight);
+ ContactGeometry.contactInterval cXci = cXcgeom.mapFor(yOffset,
+ yOffset);
+ /**
+ * start and end range corresponding to the row range under the mouse at
+ * column currentX
+ */
+ int fr, to;
+ fr = Math.min(cXci.cStart, cXci.cEnd);
+ to = Math.max(cXci.cStart, cXci.cEnd);
+
+ if (evt.isControlDown())
+ {
+ ContactMatrixI matrix = av.getContactMatrix(clicked);
+
+ if (matrix != null)
{
- int currentX = getColumnForXPos(evt.getX());
- ContactListI forCurrentX = av.getContactList(aa[graphStretch],
- currentX);
- if (forCurrentX != null)
+ // simplest approach is to select all group containing column
+ if (matrix.hasGroups())
{
- ContactGeometry cXcgeom = new ContactGeometry(forCurrentX,
- aa[graphStretch].graphHeight);
- ContactGeometry.contactInterval cXci = cXcgeom.mapFor(yOffset,
- yOffset);
- int fr, to;
- fr = Math.min(cXci.cStart, cXci.cEnd);
- to = Math.max(cXci.cStart, cXci.cEnd);
+ SequenceI rseq = clicked.sequenceRef;
+ BitSet grp = matrix.getGroupsFor(currentX);
for (int c = fr; c <= to; c++)
{
- av.getColumnSelection().addElement(c);
+ BitSet additionalGrp = matrix.getGroupsFor(c);
+ grp.or(additionalGrp);
+ }
+ HiddenColumns hc = av.getAlignment().getHiddenColumns();
+ for (int p = grp.nextSetBit(0); p >= 0; p = grp
+ .nextSetBit(p + 1))
+ {
+ int offp = (rseq != null)
+ ? rseq.findIndex(rseq.getStart() - 1 + p)
+ : p;
+
+ if (!av.hasHiddenColumns() || hc.isVisible(offp))
+ {
+ av.getColumnSelection().addElement(offp);
+ }
+ }
+ }
+ // possible alternative for interactive selection - threshold
+ // gives 'ceiling' for forming a cluster
+ // when a row+column is selected, farthest common ancestor less
+ // than thr is used to compute cluster
+
+ }
+ }
+ else
+ {
+ // select corresponding range in segment under mouse
+ {
+ for (int c = fr; c <= to; c++)
+ {
+ av.getColumnSelection().addElement(c);
+ }
+ av.getColumnSelection().addElement(currentX);
+ }
+ // PAE SPECIFIC
+ // and also select everything lower than the max range adjacent
+ // (kind of works)
+ if (PAEContactMatrix.PAEMATRIX.equals(clicked.getCalcId()))
+ {
+ int c = fr - 1;
+ ContactRange cr = forCurrentX.getRangeFor(fr, to);
+ double cval;
+ // TODO: could use GraphLine instead of arbitrary picking
+ // TODO: could report mean/median/variance for partitions
+ // (contiguous selected vs unselected regions and inter-contig
+ // regions)
+ // controls feathering - what other elements in row/column
+ // should we select
+ double thresh = cr.getMean() + (cr.getMax() - cr.getMean()) * .15;
+ while (c > 0)
+ {
+ cval = forCurrentX.getContactAt(c);
+ if (// cr.getMin() <= cval &&
+ cval <= thresh)
+ {
+ av.getColumnSelection().addElement(c--);
+ }
+ else
+ {
+ break;
+ }
+ }
+ c = to;
+ while (c < forCurrentX.getContactHeight())
+ {
+ cval = forCurrentX.getContactAt(c);
+ if (// cr.getMin() <= cval &&
+ cval <= thresh)
+ {
+ av.getColumnSelection().addElement(c++);
+ }
+ else
+ {
+ break;
}
- av.getColumnSelection().addElement(currentX);
}
}
}
}
- else
- {
- ap.getScalePanel().mousePressed(evt);
- }
+ ap.paintAlignment(false, false);
+ PaintRefresher.Refresh(ap, av.getSequenceSetId());
+ av.sendSelection();
+ return true;
}
/**
@@ -695,7 +826,10 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
ap.adjustAnnotationHeight();
}
dragMode = DragMode.Undefined;
- ap.getScalePanel().mouseReleased(evt);
+ if (!matrix_clicked(evt))
+ {
+ ap.getScalePanel().mouseReleased(evt);
+ }
/*
* isPopupTrigger is set in mouseReleased on Windows
@@ -776,12 +910,13 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
* mostly vertical drag
*/
dragMode = DragMode.Resize;
+ notJustOne = evt.isShiftDown();
/*
* but could also be a matrix drag
*/
if ((evt.isAltDown() || evt.isAltGraphDown()) && (av.getAlignment()
- .getAlignmentAnnotation()[graphStretch].graph == AlignmentAnnotation.CUSTOMRENDERER))
+ .getAlignmentAnnotation()[graphStretch].graph == AlignmentAnnotation.CONTACT_MAP))
{
/*
* dragging in a matrix
@@ -816,7 +951,20 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
AlignmentAnnotation graphAnnotation = av.getAlignment()
.getAlignmentAnnotation()[graphStretch];
int newHeight = Math.max(0, graphAnnotation.graphHeight + deltaY);
- graphAnnotation.graphHeight = newHeight;
+ if (notJustOne)
+ {
+ for (AlignmentAnnotation similar : av.getAlignment()
+ .findAnnotations(null, graphAnnotation.getCalcId(),
+ graphAnnotation.label))
+ {
+ similar.graphHeight = newHeight;
+ }
+
+ }
+ else
+ {
+ graphAnnotation.graphHeight = newHeight;
+ }
adjustPanelHeight();
ap.paintAlignment(false, false);
}
@@ -865,12 +1013,13 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
if (rowIndex == null || toRowIndex == null)
{
- System.out.println("Drag out of range. needs to be clipped");
+ jalview.bin.Console.trace("Drag out of range. needs to be clipped");
}
if (rowIndex[0] != toRowIndex[0])
{
- System.out.println("Drag went to another row. needs to be clipped");
+ jalview.bin.Console
+ .trace("Drag went to another row. needs to be clipped");
}
// rectangular selection on matrix style annotation
@@ -889,34 +1038,52 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
ContactGeometry lastXcgeom = new ContactGeometry(forFromX,
cma.graphHeight);
ContactGeometry.contactInterval lastXci = lastXcgeom
- .mapFor(rowIndex[1], rowIndex[1] + deltaY);
+ .mapFor(rowIndex[1], rowIndex[1] - deltaY);
+
ContactGeometry cXcgeom = new ContactGeometry(forToX,
cma.graphHeight);
ContactGeometry.contactInterval cXci = cXcgeom.mapFor(rowIndex[1],
- rowIndex[1] + deltaY);
+ rowIndex[1] - deltaY);
+
// mark rectangular region formed by drag
- System.err.println("Matrix Selection from last(" + lastXci.cStart
- + "," + lastXci.cEnd + ") to cur(" + cXci.cStart + ","
- + cXci.cEnd + ")");
+ jalview.bin.Console.trace("Matrix Selection from last(" + fromXc
+ + ",[" + lastXci.cStart + "," + lastXci.cEnd + "]) to cur("
+ + toXc + ",[" + cXci.cStart + "," + cXci.cEnd + "])");
int fr, to;
fr = Math.min(lastXci.cStart, lastXci.cEnd);
to = Math.max(lastXci.cStart, lastXci.cEnd);
- System.err.println("Marking " + fr + " to " + to);
+ jalview.bin.Console.trace("Marking " + fr + " to " + to);
for (int c = fr; c <= to; c++)
{
- av.getColumnSelection().addElement(c);
+ if (cma.sequenceRef != null)
+ {
+ int col = cma.sequenceRef.findIndex(c);
+ av.getColumnSelection().addElement(col);
+ }
+ else
+ {
+ av.getColumnSelection().addElement(c);
+ }
}
fr = Math.min(cXci.cStart, cXci.cEnd);
to = Math.max(cXci.cStart, cXci.cEnd);
- System.err.println("Marking " + fr + " to " + to);
+ jalview.bin.Console.trace("Marking " + fr + " to " + to);
for (int c = fr; c <= to; c++)
{
- av.getColumnSelection().addElement(c);
+ if (cma.sequenceRef != null)
+ {
+ int col = cma.sequenceRef.findIndex(c);
+ av.getColumnSelection().addElement(col);
+ }
+ else
+ {
+ av.getColumnSelection().addElement(c);
+ }
}
fr = Math.min(lastX, currentX);
to = Math.max(lastX, currentX);
- System.err.println("Marking " + fr + " to " + to);
+ jalview.bin.Console.trace("Marking " + fr + " to " + to);
for (int c = fr; c <= to; c++)
{
av.getColumnSelection().addElement(c);
@@ -1001,15 +1168,14 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
static int[] getRowIndexAndOffset(int yPos, AlignmentAnnotation[] aa)
{
int[] res = new int[2];
+ res[0] = -1;
+ res[1] = 0;
if (aa == null)
{
- res[0] = -1;
- res[1] = 0;
return res;
}
int row = -1;
int height = 0, lheight = 0;
-
for (int i = 0; i < aa.length; i++)
{
if (aa[i].visible)
@@ -1074,20 +1240,22 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
tooltip = ann.annotations[column].description;
}
// TODO abstract tooltip generator so different implementations can be built
- if (ann.graph == AlignmentAnnotation.CUSTOMRENDERER)
+ if (ann.graph == AlignmentAnnotation.CONTACT_MAP)
{
ContactListI clist = av.getContactList(ann, column);
if (clist != null)
{
ContactGeometry cgeom = new ContactGeometry(clist, ann.graphHeight);
- ContactGeometry.contactInterval ci = cgeom.mapFor(rowAndOffset,
- rowAndOffset);
+ ContactGeometry.contactInterval ci = cgeom.mapFor(rowAndOffset);
ContactRange cr = clist.getRangeFor(ci.cStart, ci.cEnd);
- tooltip = "Contact from " + ci.cStart + " to " + ci.cEnd
- + "
Mean:" + cr.getMean();
-
- // ap.getStructureSelectionManager().mouseOverSequence(ann.sequenceRef,
- // new int[] {column, ci.cStart,ci.cEnd}, -1, null)
+ tooltip = "Contact from " + clist.getPosition() + ", [" + ci.cStart
+ + " - " + ci.cEnd + "]" + "
Mean:" + cr.getMean();
+ int col = ann.sequenceRef.findPosition(column);
+ ap.getStructureSelectionManager()
+ .highlightPositionsOn(ann.sequenceRef, new int[][]
+ { new int[] { col, col },
+ new int[]
+ { ci.cStart, ci.cEnd } }, null);
}
}
return tooltip;
@@ -1239,8 +1407,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
return;
}
}
- imgWidth = (av.getRanges().getEndRes() - av.getRanges().getStartRes()
- + 1) * av.getCharWidth();
+ updateFadedImageWidth();
if (imgWidth < 1)
{
return;
@@ -1249,24 +1416,37 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
if (image == null || imgWidth != image.getWidth(this)
|| image.getHeight(this) != getHeight())
{
- try
- {
- image = new BufferedImage(imgWidth,
- ap.getAnnotationPanel().getHeight(),
- BufferedImage.TYPE_INT_RGB);
- } catch (OutOfMemoryError oom)
+ boolean tried = false;
+ image = null;
+ while (image == null && !tried)
{
try
{
- System.gc();
- } catch (Exception x)
+ image = new BufferedImage(imgWidth,
+ ap.getAnnotationPanel().getHeight(),
+ BufferedImage.TYPE_INT_RGB);
+ tried = true;
+ } catch (IllegalArgumentException exc)
+ {
+ System.err.println(
+ "Serious issue with viewport geometry imgWidth requested was "
+ + imgWidth);
+ return;
+ } catch (OutOfMemoryError oom)
{
+ try
+ {
+ System.gc();
+ } catch (Exception x)
+ {
+ }
+ ;
+ new OOMWarning(
+ "Couldn't allocate memory to redraw screen. Please restart Jalview",
+ oom);
+ return;
}
- ;
- new OOMWarning(
- "Couldn't allocate memory to redraw screen. Please restart Jalview",
- oom);
- return;
+
}
gg = (Graphics2D) image.getGraphics();
@@ -1295,6 +1475,13 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
g.drawImage(image, 0, 0, this);
}
+ public void updateFadedImageWidth()
+ {
+ imgWidth = (av.getRanges().getEndRes() - av.getRanges().getStartRes()
+ + 1) * av.getCharWidth();
+
+ }
+
/**
* set true to enable redraw timing debug output on stderr
*/
@@ -1470,6 +1657,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
@Override
public int getFadedImageWidth()
{
+ updateFadedImageWidth();
return imgWidth;
}