From: Jim Procter Date: Tue, 2 Aug 2016 10:05:53 +0000 (+0100) Subject: Merge branch 'develop' into efficiency/JAL-2034_JAL-1421 X-Git-Tag: Release_2_10_0~120^2~2 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=0f40a8334651302a74a223ecd3e583451302bb42;hp=6058cdbed98274bcc81d39608c1a35c95c6fd33f;p=jalview.git Merge branch 'develop' into efficiency/JAL-2034_JAL-1421 --- diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index cbb5c99..849c05c 100644 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -2234,7 +2234,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } sg.setEndRes(viewport.getAlignment().getWidth() - 1); viewport.setSelectionGroup(sg); - alignPanel.paintAlignment(true); + // JAL-2034 - should delegate to + // alignPanel to decide if overview needs + // updating. + alignPanel.paintAlignment(false); PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); viewport.sendSelection(); } @@ -2251,7 +2254,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, viewport.setSelectionGroup(null); alignPanel.idPanel.idCanvas.searchResults = null; alignPanel.seqPanel.seqCanvas.highlightSearchResults(null); - alignPanel.paintAlignment(true); + // JAL-2034 - should delegate to + // alignPanel to decide if overview needs + // updating. + alignPanel.paintAlignment(false); PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); viewport.sendSelection(); } diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java index 5a1243a..9b2be4c 100755 --- a/src/jalview/appletgui/OverviewPanel.java +++ b/src/jalview/appletgui/OverviewPanel.java @@ -305,6 +305,10 @@ public class OverviewPanel extends Panel implements Runnable, AlignmentI alignment = av.getAlignment(); for (row = 0; row <= sequencesHeight; row++) { + if (resizeAgain) + { + break; + } if ((int) (row * sampleRow) == lastrow) { sameRow++; @@ -386,6 +390,10 @@ public class OverviewPanel extends Panel implements Runnable, { for (col = 0; col < width; col++) { + if (resizeAgain) + { + break; + } lastcol = (int) (col * sampleCol); { mg.translate(col, sequencesHeight); diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java index 31bf6a4..02172d6 100644 --- a/src/jalview/appletgui/SeqPanel.java +++ b/src/jalview/appletgui/SeqPanel.java @@ -919,6 +919,21 @@ public class SeqPanel extends Panel implements MouseMotionListener, Tooltip tooltip; + /** + * set when the current UI interaction has resulted in a change that requires + * overview shading to be recalculated. this could be changed to something + * more expressive that indicates what actually has changed, so selective + * redraws can be applied + */ + private boolean needOverviewUpdate; // TODO: refactor to avcontroller + + /** + * set if av.getSelectionGroup() refers to a group that is defined on the + * alignment view, rather than a transient selection + */ + private boolean editingDefinedGroup = false; // TODO: refactor to avcontroller + // or viewModel + @Override public void mouseDragged(MouseEvent evt) { @@ -1421,10 +1436,12 @@ public class SeqPanel extends Panel implements MouseMotionListener, && res < stretchGroup.getEndRes()) { av.setSelectionGroup(stretchGroup); + editingDefinedGroup = true; } else { stretchGroup = null; + editingDefinedGroup = false; } } @@ -1444,6 +1461,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, && allGroups[i].getEndRes() >= res) { stretchGroup = allGroups[i]; + editingDefinedGroup = true; break; } } @@ -1499,6 +1517,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, sg.setEndRes(res); sg.addSequence(sequence, false); av.setSelectionGroup(sg); + editingDefinedGroup = false; stretchGroup = sg; if (av.getConservationSelected()) @@ -1521,9 +1540,10 @@ public class SeqPanel extends Panel implements MouseMotionListener, { return; } - - stretchGroup.recalcConservation(); // always do this - annotation has own - // state + // always do this - annotation has own state + // but defer colourscheme update until hidden sequences are passed in + boolean vischange = stretchGroup.recalcConservation(true); + needOverviewUpdate |= vischange && editingDefinedGroup; if (stretchGroup.cs != null) { stretchGroup.cs.alignmentChanged(stretchGroup, @@ -1540,11 +1560,13 @@ public class SeqPanel extends Panel implements MouseMotionListener, stretchGroup.getName()); } } + PaintRefresher.Refresh(ap, av.getSequenceSetId()); + ap.paintAlignment(needOverviewUpdate); + needOverviewUpdate =false; + editingDefinedGroup = false; changeEndRes = false; changeStartRes = false; stretchGroup = null; - PaintRefresher.Refresh(ap, av.getSequenceSetId()); - ap.paintAlignment(true); av.sendSelection(); } @@ -1596,6 +1618,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, if (res > (stretchGroup.getStartRes() - 1)) { stretchGroup.setEndRes(res); + needOverviewUpdate |= editingDefinedGroup; } } else if (changeStartRes) @@ -1603,6 +1626,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, if (res < (stretchGroup.getEndRes() + 1)) { stretchGroup.setStartRes(res); + needOverviewUpdate |= editingDefinedGroup; } } @@ -1636,6 +1660,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, if (stretchGroup.getSequences(null).contains(nextSeq)) { stretchGroup.deleteSequence(seq, false); + needOverviewUpdate |= editingDefinedGroup; } else { @@ -1645,6 +1670,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, } stretchGroup.addSequence(nextSeq, false); + needOverviewUpdate |= editingDefinedGroup; } } diff --git a/src/jalview/datamodel/AlignmentView.java b/src/jalview/datamodel/AlignmentView.java index 756a116..fa72e80 100644 --- a/src/jalview/datamodel/AlignmentView.java +++ b/src/jalview/datamodel/AlignmentView.java @@ -26,7 +26,6 @@ import jalview.util.ShiftList; import java.io.PrintStream; import java.util.ArrayList; import java.util.List; -import java.util.Vector; /** * Transient object compactly representing a 'view' of an alignment - with @@ -69,13 +68,51 @@ public class AlignmentView */ private class ScGroup { - public Vector seqs; + public List seqs; public SequenceGroup sg; ScGroup() { - seqs = new Vector(); + seqs = new ArrayList(); + } + + /** + * @param seq + * @return true if seq was not a member before and was added to group + */ + public boolean add(SeqCigar seq) + { + if (!seq.isMemberOf(this)) + { + seqs.add(seq); + seq.setGroupMembership(this); + return true; + } + else + { + return false; + } + } + + /** + * + * @param seq + * @return true if seq was a member and was removed from group + */ + public boolean remove(SeqCigar seq) + { + if (seq.removeGroupMembership(this)) + { + seqs.remove(seq); + return true; + } + return false; + } + + public int size() + { + return seqs.size(); } } @@ -83,7 +120,7 @@ public class AlignmentView * vector of selected seqCigars. This vector is also referenced by each * seqCigar contained in it. */ - private Vector selected; + private ScGroup selected; /** * Construct an alignmentView from a live jalview alignment view. Note - @@ -124,7 +161,7 @@ public class AlignmentView if (selection != null && selection.getSize() > 0) { List sel = selection.getSequences(null); - this.selected = new Vector(); + this.selected = new ScGroup(); selseqs = selection .getSequencesInOrder(alignment, selectedRegionOnly); } @@ -194,8 +231,7 @@ public class AlignmentView if (selection != null && selection.getSize() > 0 && !selectedRegionOnly) { - sequences[csi].setGroupMembership(selected); - selected.addElement(sequences[csi]); + selected.add(sequences[csi]); } if (seqsets != null) { @@ -203,9 +239,8 @@ public class AlignmentView { if ((seqsets.get(sg)).contains(selseqs[i])) { - sequences[csi].setGroupMembership(sgrps[sg]); sgrps[sg].sg.deleteSequence(selseqs[i], false); - sgrps[sg].seqs.addElement(sequences[csi]); + sgrps[sg].add(sequences[csi]); if (!addedgps[sg]) { if (scGroups == null) @@ -1073,10 +1108,10 @@ public class AlignmentView + sgr.sg.getEndRes()); for (int s = 0; s < sgr.seqs.size(); s++) { - if (!((SeqCigar) sgr.seqs.elementAt(s)).isMemberOf(sgr)) + // JBPnote this should be a unit test for ScGroup + if (!sgr.seqs.get(s).isMemberOf(sgr)) { - os.println("** WARNING: sequence " - + ((SeqCigar) sgr.seqs.elementAt(s)).toString() + os.println("** WARNING: sequence " + sgr.seqs.get(s).toString() + " is not marked as member of group."); } } diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java index d403d6e..22c537a 100755 --- a/src/jalview/datamodel/SequenceGroup.java +++ b/src/jalview/datamodel/SequenceGroup.java @@ -504,14 +504,31 @@ public class SequenceGroup implements AnnotatedCollectionI } /** - * calculate residue conservation for group - but only if necessary. + * calculate residue conservation and colourschemes for group - but only if + * necessary. returns true if the calculation resulted in a visible change to + * group */ - public void recalcConservation() + public boolean recalcConservation() + { + return recalcConservation(false); + } + + /** + * calculate residue conservation for group - but only if necessary. returns + * true if the calculation resulted in a visible change to group + * + * @param defer + * when set, colourschemes for this group are not refreshed after + * recalculation + */ + public boolean recalcConservation(boolean defer) { if (cs == null && consensus == null && conservation == null) { - return; + return false; } + // TODO: try harder to detect changes in state in order to minimise + // recalculation effort try { Hashtable cnsns[] = AAFrequency.calculate(sequences, startRes, @@ -545,16 +562,22 @@ public class SequenceGroup implements AnnotatedCollectionI } } } - if (cs != null) + if (cs != null && !defer) { + // TODO: JAL-2034 should cs.alignmentChanged modify return state cs.alignmentChanged(context != null ? context : this, null); + return true; + } + else + { + return false; } } catch (java.lang.OutOfMemoryError err) { // TODO: catch OOM System.out.println("Out of memory loading groups: " + err); } - + return false; } private void _updateConservationRow(Conservation c) diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 15f88fb..b0debf8 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -2434,7 +2434,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, sg.setEndRes(viewport.getAlignment().getWidth() - 1); viewport.setSelectionGroup(sg); viewport.sendSelection(); - alignPanel.paintAlignment(true); + // JAL-2034 - should delegate to + // alignPanel to decide if overview needs + // updating. + alignPanel.paintAlignment(false); PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); } @@ -2457,7 +2460,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.setSelectionGroup(null); alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null); alignPanel.getIdPanel().getIdCanvas().searchResults = null; - alignPanel.paintAlignment(true); + // JAL-2034 - should delegate to + // alignPanel to decide if overview needs + // updating. + alignPanel.paintAlignment(false); PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); viewport.sendSelection(); } @@ -2484,6 +2490,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false); } + // JAL-2034 - should delegate to + // alignPanel to decide if overview needs + // updating. alignPanel.paintAlignment(true); PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java index de0dbe5..c2a401d 100755 --- a/src/jalview/gui/OverviewPanel.java +++ b/src/jalview/gui/OverviewPanel.java @@ -295,14 +295,25 @@ public class OverviewPanel extends JPanel implements Runnable final boolean hasHiddenRows = av.hasHiddenRows(), hasHiddenCols = av .hasHiddenColumns(); boolean hiddenRow = false; + // get hidden row and hidden column map once at beginning. + // clone featureRenderer settings to avoid race conditions... if state is + // updated just need to refresh again for (row = 0; row < sequencesHeight; row++) { + if (resizeAgain) + { + break; + } if ((int) (row * sampleRow) == lastrow) { // No need to recalculate the colours, // Just copy from the row above for (col = 0; col < width; col++) { + if (resizeAgain) + { + break; + } miniMe.setRGB(col, row, miniMe.getRGB(col, row - 1)); } continue; @@ -340,6 +351,10 @@ public class OverviewPanel extends JPanel implements Runnable for (col = 0; col < width; col++) { + if (resizeAgain) + { + break; + } if ((int) (col * sampleCol) == lastcol && (int) (row * sampleRow) == lastrow) { @@ -380,6 +395,10 @@ public class OverviewPanel extends JPanel implements Runnable renderer.updateFromAlignViewport(av); for (col = 0; col < width; col++) { + if (resizeAgain) + { + break; + } lastcol = (int) (col * sampleCol); { mg.translate(col, sequencesHeight); diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java index 2d44a0f..8ebcc87 100644 --- a/src/jalview/gui/SeqPanel.java +++ b/src/jalview/gui/SeqPanel.java @@ -825,6 +825,20 @@ public class SeqPanel extends JPanel implements MouseListener, String lastTooltip; /** + * set when the current UI interaction has resulted in a change that requires + * overview shading to be recalculated. this could be changed to something + * more expressive that indicates what actually has changed, so selective + * redraws can be applied + */ + private boolean needOverviewUpdate = false; // TODO: refactor to avcontroller + + /** + * set if av.getSelectionGroup() refers to a group that is defined on the + * alignment view, rather than a transient selection + */ + private boolean editingDefinedGroup = false; // TODO: refactor to avcontroller or viewModel + + /** * Set status message in alignment panel * * @param sequence @@ -1568,10 +1582,12 @@ public class SeqPanel extends JPanel implements MouseListener, && (res < stretchGroup.getEndRes())) { av.setSelectionGroup(stretchGroup); + editingDefinedGroup = true; } else { stretchGroup = null; + editingDefinedGroup = false; } } else if (!stretchGroup.getSequences(null).contains(sequence) @@ -1590,6 +1606,7 @@ public class SeqPanel extends JPanel implements MouseListener, && (allGroups[i].getEndRes() >= res)) { stretchGroup = allGroups[i]; + editingDefinedGroup = true; break; } } @@ -1639,7 +1656,7 @@ public class SeqPanel extends JPanel implements MouseListener, sg.setEndRes(res); sg.addSequence(sequence, false); av.setSelectionGroup(sg); - + editingDefinedGroup = false; stretchGroup = sg; if (av.getConservationSelected()) @@ -1682,9 +1699,10 @@ public class SeqPanel extends JPanel implements MouseListener, { return; } - - stretchGroup.recalcConservation(); // always do this - annotation has own - // state + // always do this - annotation has own state + // but defer colourscheme update until hidden sequences are passed in + boolean vischange = stretchGroup.recalcConservation(true); + needOverviewUpdate |= vischange && editingDefinedGroup; if (stretchGroup.cs != null) { stretchGroup.cs.alignmentChanged(stretchGroup, @@ -1702,8 +1720,9 @@ public class SeqPanel extends JPanel implements MouseListener, } } PaintRefresher.Refresh(this, av.getSequenceSetId()); - ap.paintAlignment(true); - + ap.paintAlignment(needOverviewUpdate); + needOverviewUpdate =false; + editingDefinedGroup = false; changeEndRes = false; changeStartRes = false; stretchGroup = null; @@ -1757,6 +1776,7 @@ public class SeqPanel extends JPanel implements MouseListener, if (res > (stretchGroup.getStartRes() - 1)) { stretchGroup.setEndRes(res); + needOverviewUpdate |= editingDefinedGroup; } } else if (changeStartRes) @@ -1764,6 +1784,7 @@ public class SeqPanel extends JPanel implements MouseListener, if (res < (stretchGroup.getEndRes() + 1)) { stretchGroup.setStartRes(res); + needOverviewUpdate |= editingDefinedGroup; } } @@ -1797,6 +1818,7 @@ public class SeqPanel extends JPanel implements MouseListener, if (stretchGroup.getSequences(null).contains(nextSeq)) { stretchGroup.deleteSequence(seq, false); + needOverviewUpdate |= editingDefinedGroup; } else { @@ -1806,6 +1828,7 @@ public class SeqPanel extends JPanel implements MouseListener, } stretchGroup.addSequence(nextSeq, false); + needOverviewUpdate |= editingDefinedGroup; } } diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java index 427eb08..64fe053 100755 --- a/src/jalview/gui/SequenceRenderer.java +++ b/src/jalview/gui/SequenceRenderer.java @@ -85,6 +85,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer @Override public Color getResidueBoxColour(SequenceI seq, int i) { + // rate limiting step when rendering overview for lots of groups allGroups = av.getAlignment().findAllGroups(seq); if (inCurrentSequenceGroup(i))