*/
package jalview.api;
+import java.awt.Color;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+
import jalview.analysis.Conservation;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.schemes.ColourSchemeI;
-import java.awt.Color;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Map;
-
/**
* @author jimp
*
* @return
*/
String getViewId();
+
+ /**
+ * Return true if view should scroll to show the highlighted region of a
+ * sequence
+ *
+ * @return
+ */
+ boolean isFollowHighlight();
+
+ /**
+ * Set whether view should scroll to show the highlighted region of a sequence
+ */
+ void setFollowHighlight(boolean b);
}
import jalview.structures.models.AAStructureBindingModel;
import jalview.util.MappingUtils;
import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
public class AlignFrame extends EmbmenuFrame implements ActionListener,
ItemListener, KeyListener, AlignViewControllerGuiI
viewport.updateConsensus(alignPanel);
displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
- followMouseOverFlag.setState(viewport.getFollowHighlight());
+ followMouseOverFlag.setState(viewport.isFollowHighlight());
showGroupConsensus.setState(viewport.isShowGroupConsensus());
showGroupConservation.setState(viewport.isShowGroupConservation());
showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
private void mouseOverFlag_stateChanged()
{
- viewport.followHighlight = followMouseOverFlag.getState();
+ viewport.setFollowHighlight(followMouseOverFlag.getState());
// TODO: could kick the scrollTo mechanism to reset view for current
// searchresults.
}
viewport.addToRedoList(command);
command.undoCommand(null);
- AlignViewport originalSource = getOriginatingSource(command);
+ AlignmentViewport originalSource = getOriginatingSource(command);
// JBPNote Test
if (originalSource != viewport)
{
viewport.addToHistoryList(command);
command.doCommand(null);
- AlignViewport originalSource = getOriginatingSource(command);
+ AlignmentViewport originalSource = getOriginatingSource(command);
// JBPNote Test
if (originalSource != viewport)
{
.getAlignment().getSequences());
}
- AlignViewport getOriginatingSource(CommandI command)
+ AlignmentViewport getOriginatingSource(CommandI command)
{
- AlignViewport originalSource = null;
+ AlignmentViewport originalSource = null;
// For sequence removal and addition, we need to fire
// the property change event FROM the viewport where the
// original alignment was altered
import jalview.commands.CommandI;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SearchResults;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
public class AlignViewport extends AlignmentViewport implements
AlignViewportI, SelectionSource, VamsasSource, CommandListener
{
- int startRes;
-
- int endRes;
-
- int startSeq;
-
- int endSeq;
-
boolean cursorMode = false;
Font font = new Font("SansSerif", Font.PLAIN, 10);
+ widthScale + "). Ignoring.");
widthScale = 1;
}
- if (applet.debug)
+ if (JalviewLite.debug)
{
System.err
.println("Alignment character width scaling factor is now "
+ heightScale + "). Ignoring.");
heightScale = 1;
}
- if (applet.debug)
+ if (JalviewLite.debug)
{
System.err
.println("Alignment character height scaling factor is now "
}
sortByTree = applet.getDefaultParameter("sortByTree", sortByTree);
- followHighlight = applet.getDefaultParameter("automaticScrolling",
- followHighlight);
- followSelection = followHighlight;
+ setFollowHighlight(applet.getDefaultParameter("automaticScrolling",
+ isFollowHighlight()));
+ followSelection = isFollowHighlight();
showSequenceLogo = applet.getDefaultParameter("showSequenceLogo",
showSequenceLogo);
return sq;
}
- public int getStartRes()
- {
- return startRes;
- }
-
- public int getEndRes()
- {
- return endRes;
- }
-
- public int getStartSeq()
- {
- return startSeq;
- }
-
- public void setStartRes(int res)
- {
- this.startRes = res;
- }
-
- public void setStartSeq(int seq)
- {
- this.startSeq = seq;
- }
-
- public void setEndRes(int res)
- {
- if (res > alignment.getWidth() - 1)
- {
- // log.System.out.println(" Corrected res from " + res + " to maximum " +
- // (alignment.getWidth()-1));
- res = alignment.getWidth() - 1;
- }
- if (res < 0)
- {
- res = 0;
- }
- this.endRes = res;
- }
-
- public void setEndSeq(int seq)
- {
- if (seq > alignment.getHeight())
- {
- seq = alignment.getHeight();
- }
- if (seq < 0)
- {
- seq = 0;
- }
- this.endSeq = seq;
- }
-
- public int getEndSeq()
- {
- return endSeq;
- }
-
java.awt.Frame nullFrame;
protected FeatureSettings featureSettings = null;
return centreColumnLabels;
}
- public boolean followHighlight = true;
-
- public boolean getFollowHighlight()
- {
- return followHighlight;
- }
-
public boolean followSelection = true;
/**
return this;
}
+ /**
+ * If this viewport has a (Protein/cDNA) complement, then scroll the
+ * complementary alignment to match this one.
+ */
+ public void scrollComplementaryAlignment(AlignmentPanel complementPanel)
+ {
+ if (complementPanel == null)
+ {
+ return;
+ }
+
+ /*
+ * Populate a SearchResults object with the mapped location to scroll to. If
+ * there is no complement, or it is not following highlights, or no mapping
+ * is found, the result will be empty.
+ */
+ SearchResults sr = new SearchResults();
+ int seqOffset = findComplementScrollTarget(sr);
+ if (!sr.isEmpty())
+ {
+ complementPanel.setFollowingComplementScroll(true);
+ complementPanel.scrollToCentre(sr, seqOffset);
+ }
+ }
+
}
import java.awt.event.AdjustmentListener;
import java.awt.event.ComponentAdapter;
import java.awt.event.ComponentEvent;
+import java.util.List;
import jalview.analysis.AnnotationSorter;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
+import jalview.bin.JalviewLite;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SequenceI;
public boolean scrollToPosition(SearchResults results,
boolean redrawOverview)
{
+ return scrollToPosition(results, redrawOverview, false);
+ }
+ /**
+ * 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)
+ * @return false if results were not found
+ */
+ public boolean scrollToPosition(SearchResults results,
+ boolean redrawOverview, boolean centre)
+ {
// do we need to scroll the panel?
if (results != null && results.getSize() > 0)
{
int[] r = results.getResults(seq, 0, alignment.getWidth());
if (r == null)
{
- if (av.applet.debug)
+ if (JalviewLite.debug)
{// DEBUG
System.out
.println("DEBUG: scroll didn't happen - results not within alignment : "
}
return false;
}
- if (av.applet.debug)
+ if (JalviewLite.debug)
{
// DEBUG
/*
}
int start = r[0];
int end = r[1];
+
+ /*
+ * To centre results, scroll to positions half the visible width
+ * left/right of the start/end positions
+ */
+ if (centre)
+ {
+ int offset = (av.getEndRes() - av.getStartRes() + 1) / 2 - 1;
+ start = Math.max(start - offset, 0);
+ end = Math.min(end + offset, seq.getEnd() - 1);
+ }
+
if (start < 0)
{
return false;
* 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)
- {
- start = 0;
- }
+ // below is scrolling logic up to Jalview 2.8.2
+ // 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)
+ // {
+ // start = 0;
+ // }
+ //
+ // }
+ // if (seqIndex > av.getAlignment().getHeight() - vextent)
+ // {
+ // seqIndex = av.getAlignment().getHeight() - vextent;
+ // if (seqIndex < 0)
+ // {
+ // seqIndex = 0;
+ // }
+ // }
+ // setScrollValues(start, seqIndex);
+ // }
+ // logic copied from jalview.gui.AlignmentPanel:
+ if ((startv = av.getStartRes()) >= start)
+ {
+ /*
+ * Scroll left to make start of search results visible
+ */
+ setScrollValues(start - 1, seqIndex);
+ }
+ else if ((endv = av.getEndRes()) <= end)
+ {
+ /*
+ * Scroll right to make end of search results visible
+ */
+ setScrollValues(startv + 1 + end - endv, seqIndex);
+ }
+ else if ((starts = av.getStartSeq()) > seqIndex)
+ {
+ /*
+ * Scroll up to make start of search results visible
+ */
+ setScrollValues(av.getStartRes(), seqIndex);
}
- if (seqIndex > av.getAlignment().getHeight() - vextent)
+ else if ((ends = av.getEndSeq()) <= seqIndex)
{
- seqIndex = av.getAlignment().getHeight() - vextent;
- if (seqIndex < 0)
- {
- seqIndex = 0;
- }
+ /*
+ * Scroll down to make end of search results visible
+ */
+ setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1);
}
- // System.out.println("trying to scroll to: "+start+" "+seqIndex);
- setScrollValues(start, seqIndex);
- }/**/
+ /*
+ * Else results are already visible - no need to scroll
+ */
}
else
{
}
sendViewPosition();
+ /*
+ * If there is one, scroll the (Protein/cDNA) complementary alignment to
+ * match, unless we are ourselves doing that.
+ */
+ if (isFollowingComplementScroll())
+ {
+ setFollowingComplementScroll(false);
+ }
+ else
+ {
+ AlignmentPanel ap = getComplementPanel();
+ av.scrollComplementaryAlignment(ap);
+ }
+
+ }
+
+ /**
+ * A helper method to return the AlignmentPanel in the other (complementary)
+ * half of a SplitFrame view. Returns null if not in a SplitFrame.
+ *
+ * @return
+ */
+ private AlignmentPanel getComplementPanel()
+ {
+ AlignmentPanel ap = null;
+ if (alignFrame != null)
+ {
+ SplitFrame sf = alignFrame.getSplitFrame();
+ if (sf != null)
+ {
+ AlignFrame other = sf.getComplement(alignFrame);
+ if (other != null)
+ {
+ ap = other.alignPanel;
+ }
+ }
+ }
+ return ap;
+ }
+
+ /**
+ * Follow a scrolling change in the (cDNA/Protein) complementary alignment.
+ * The aim is to keep the two alignments 'lined up' on their centre columns.
+ *
+ * @param sr
+ * holds mapped region(s) of this alignment that we are scrolling
+ * 'to'; may be modified for sequence offset by this method
+ * @param seqOffset
+ * the number of visible sequences to show above the mapped region
+ */
+ protected void scrollToCentre(SearchResults sr, int seqOffset)
+ {
+ /*
+ * To avoid jumpy vertical scrolling (if some sequences are gapped or not
+ * mapped), we can make the scroll-to location a sequence above the one
+ * actually mapped.
+ */
+ SequenceI mappedTo = sr.getResultSequence(0);
+ List<SequenceI> seqs = av.getAlignment().getSequences();
+
+ /*
+ * This is like AlignmentI.findIndex(seq) but here we are matching the
+ * dataset sequence not the aligned sequence
+ */
+ int sequenceIndex = 0;
+ boolean matched = false;
+ for (SequenceI seq : seqs)
+ {
+ if (mappedTo == seq.getDatasetSequence())
+ {
+ matched = true;
+ break;
+ }
+ sequenceIndex++;
+ }
+ if (!matched)
+ {
+ return; // failsafe, shouldn't happen
+ }
+ sequenceIndex = Math.max(0, sequenceIndex - seqOffset);
+ sr.getResults().get(0)
+ .setSequence(av.getAlignment().getSequenceAt(sequenceIndex));
+
+ /*
+ * Scroll to position but centring the target residue. Also set a state flag
+ * to prevent adjustmentValueChanged performing this recursively.
+ */
+ setFollowingComplementScroll(true);
+ scrollToPosition(sr, true, true);
}
private void sendViewPosition()
protected Panel seqPanelHolder = new Panel();
- BorderLayout borderLayout1 = new BorderLayout();
-
- BorderLayout borderLayout3 = new BorderLayout();
-
protected Panel scalePanelHolder = new Panel();
protected Panel idPanelHolder = new Panel();
- BorderLayout borderLayout5 = new BorderLayout();
-
protected Panel idSpaceFillerPanel1 = new Panel();
public Panel annotationSpaceFillerHolder = new Panel();
- BorderLayout borderLayout6 = new BorderLayout();
-
- BorderLayout borderLayout7 = new BorderLayout();
-
- Panel hscrollHolder = new Panel();
-
- BorderLayout borderLayout10 = new BorderLayout();
-
protected Panel hscrollFillerPanel = new Panel();
- BorderLayout borderLayout11 = new BorderLayout();
-
- BorderLayout borderLayout4 = new BorderLayout();
-
- BorderLayout borderLayout2 = new BorderLayout();
-
Panel annotationPanelHolder = new Panel();
protected Scrollbar apvscroll = new Scrollbar();
- BorderLayout borderLayout12 = new BorderLayout();
+ /*
+ * Flag set while scrolling to follow complementary cDNA/protein scroll. When
+ * true, suppresses invoking the same method recursively.
+ */
+ private boolean followingComplementScroll;
private void jbInit() throws Exception
{
// idPanelHolder.setPreferredSize(new Dimension(70, 10));
- this.setLayout(borderLayout7);
+ this.setLayout(new BorderLayout());
// sequenceHolderPanel.setPreferredSize(new Dimension(150, 150));
- sequenceHolderPanel.setLayout(borderLayout3);
- seqPanelHolder.setLayout(borderLayout1);
+ sequenceHolderPanel.setLayout(new BorderLayout());
+ seqPanelHolder.setLayout(new BorderLayout());
scalePanelHolder.setBackground(Color.white);
// scalePanelHolder.setPreferredSize(new Dimension(10, 30));
- scalePanelHolder.setLayout(borderLayout6);
- idPanelHolder.setLayout(borderLayout5);
+ scalePanelHolder.setLayout(new BorderLayout());
+ idPanelHolder.setLayout(new BorderLayout());
idSpaceFillerPanel1.setBackground(Color.white);
// idSpaceFillerPanel1.setPreferredSize(new Dimension(10, 30));
- idSpaceFillerPanel1.setLayout(borderLayout11);
+ idSpaceFillerPanel1.setLayout(new BorderLayout());
annotationSpaceFillerHolder.setBackground(Color.white);
// annotationSpaceFillerHolder.setPreferredSize(new Dimension(10, 80));
- annotationSpaceFillerHolder.setLayout(borderLayout4);
+ annotationSpaceFillerHolder.setLayout(new BorderLayout());
hscroll.setOrientation(Scrollbar.HORIZONTAL);
- hscrollHolder.setLayout(borderLayout10);
+
+ Panel hscrollHolder = new Panel();
+ hscrollHolder.setLayout(new BorderLayout());
hscrollFillerPanel.setBackground(Color.white);
apvscroll.setOrientation(Scrollbar.VERTICAL);
apvscroll.setVisible(true);
apvscroll.addAdjustmentListener(this);
annotationPanelHolder.setBackground(Color.white);
- annotationPanelHolder.setLayout(borderLayout12);
+ annotationPanelHolder.setLayout(new BorderLayout());
annotationPanelHolder.add(apvscroll, BorderLayout.EAST);
// hscrollFillerPanel.setPreferredSize(new Dimension(70, 10));
hscrollHolder.setBackground(Color.white);
error.printStackTrace();
}
+ /**
+ * Set a flag to say we are scrolling to follow a (cDNA/protein) complement.
+ *
+ * @param b
+ */
+ protected void setFollowingComplementScroll(boolean b)
+ {
+ this.followingComplementScroll = b;
+ }
+
+ protected boolean isFollowingComplementScroll()
+ {
+ return this.followingComplementScroll;
+ }
+
}
import jalview.schemes.AnnotationColourGradient;
import jalview.schemes.GraduatedColor;
import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
/**
* @param av
* DOCUMENT ME!
*/
- public FeatureRenderer(AlignViewport av)
+ public FeatureRenderer(AlignmentViewport av)
{
super();
this.av = av;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
import java.awt.Button;
import java.awt.Checkbox;
public class Finder extends Panel implements ActionListener
{
- AlignViewport av;
+ AlignmentViewport av;
AlignmentPanel ap;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.util.UrlLink;
+import jalview.viewmodel.AlignmentViewport;
import java.awt.BorderLayout;
import java.awt.Panel;
protected IdCanvas idCanvas;
- protected AlignViewport av;
+ protected AlignmentViewport av;
protected AlignmentPanel alignPanel;
package jalview.appletgui;
import java.util.*;
-
import java.awt.*;
import java.awt.event.*;
import jalview.datamodel.*;
import jalview.math.*;
import jalview.util.*;
+import jalview.viewmodel.AlignmentViewport;
public class RotatableCanvas extends Panel implements MouseListener,
MouseMotionListener, KeyListener, RotatableCanvasI
float scalefactor = 1;
- AlignViewport av;
+ AlignmentViewport av;
boolean showLabels = false;
- public RotatableCanvas(AlignViewport av)
+ public RotatableCanvas(AlignmentViewport av)
{
this.av = av;
}
import jalview.datamodel.SearchResults;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.viewmodel.AlignmentViewport;
import java.awt.Color;
import java.awt.FontMetrics;
avcharWidth = av.getCharWidth();
}
- public AlignViewport getViewport()
+ public AlignmentViewport getViewport()
{
return av;
}
import jalview.structure.VamsasSource;
import jalview.util.MappingUtils;
import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
public class SeqPanel extends Panel implements MouseMotionListener,
MouseListener, SequenceListener, SelectionListener
public void highlightSequence(SearchResults results)
{
- if (av.followHighlight)
+ if (av.isFollowHighlight())
{
if (ap.scrollToPosition(results, true))
{
// TODO: extend config options to allow user to control if selections may be
// shared between viewports.
if (av != null
- && (av == source || !av.followSelection || (source instanceof AlignViewport && ((AlignViewport) source)
+ && (av == source || !av.followSelection || (source instanceof AlignViewport && ((AlignmentViewport) source)
.getSequenceSetId().equals(av.getSequenceSetId()))))
{
return;
import jalview.bin.JalviewLite;
import jalview.datamodel.AlignmentI;
import jalview.structure.StructureSelectionManager;
+import jalview.viewmodel.AlignmentViewport;
public class SplitFrame extends EmbmenuFrame
{
final AlignViewport bottomViewport = bottomFrame.viewport;
final AlignmentI topAlignment = topViewport.getAlignment();
final AlignmentI bottomAlignment = bottomViewport.getAlignment();
- AlignViewport cdna = topAlignment.isNucleotide() ? topViewport
+ AlignmentViewport cdna = topAlignment.isNucleotide() ? topViewport
: (bottomAlignment.isNucleotide() ? bottomViewport : null);
- AlignViewport protein = !topAlignment.isNucleotide() ? topViewport
+ AlignmentViewport protein = !topAlignment.isNucleotide() ? topViewport
: (!bottomAlignment.isNucleotide() ? bottomViewport : null);
boolean mapped = AlignmentUtils.mapProteinToCdna(
*/
protected void adjustLayout()
{
- AlignViewport cdna = topFrame.getAlignViewport().getAlignment()
+ AlignmentViewport cdna = topFrame.getAlignViewport().getAlignment()
.isNucleotide() ? topFrame.viewport : bottomFrame.viewport;
- AlignViewport protein = cdna == topFrame.viewport ? bottomFrame.viewport
+ AlignmentViewport protein = cdna == topFrame.viewport ? bottomFrame.viewport
: topFrame.viewport;
/*
else
{
this.add(outermost);
- int width = Math.max(topFrame.frameWidth,
- bottomFrame.frameWidth);
+ int width = Math.max(topFrame.frameWidth, bottomFrame.frameWidth);
int height = topFrame.frameHeight + bottomFrame.frameHeight;
jalview.bin.JalviewLite
.addFrame(this, this.getTitle(), width, height);
}
}
+
+ /**
+ * Returns the contained AlignFrame complementary to the one given (or null if
+ * no match to top or bottom component).
+ *
+ * @param af
+ * @return
+ */
+ public AlignFrame getComplement(AlignFrame af)
+ {
+ if (topFrame == af)
+ {
+ return bottomFrame;
+ }
+ else if (bottomFrame == af)
+ {
+ return topFrame;
+ }
+ return null;
+ }
}
import jalview.schemes.UserColourScheme;
import jalview.util.Format;
import jalview.util.MappingUtils;
+import jalview.viewmodel.AlignmentViewport;
import java.awt.Color;
import java.awt.Dimension;
ap.updateAnnotation();
if (av.getCodingComplement() != null)
{
- ((AlignViewport) av.getCodingComplement()).firePropertyChange(
+ ((AlignmentViewport) av.getCodingComplement()).firePropertyChange(
"alignment", null, ap.av.getAlignment().getSequences());
}
}
* Set the 'follow' flag on the Viewport (and scroll to position if now
* true).
*/
- if (viewport.followHighlight = this.followHighlightMenuItem.getState())
+ final boolean state = this.followHighlightMenuItem.getState();
+ viewport.setFollowHighlight(state);
+ if (state)
{
alignPanel.scrollToPosition(
alignPanel.getSeqPanel().seqCanvas.searchResults, false);
import java.awt.Rectangle;
import java.util.ArrayList;
import java.util.Hashtable;
-import java.util.List;
import java.util.Set;
import java.util.Vector;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.HiddenSequences;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SearchResults;
import jalview.datamodel.Sequence;
import jalview.structure.SelectionSource;
import jalview.structure.StructureSelectionManager;
import jalview.structure.VamsasSource;
-import jalview.util.Comparison;
-import jalview.util.MappingUtils;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
import jalview.ws.params.AutoCalcSetting;
public class AlignViewport extends AlignmentViewport implements
SelectionSource, AlignViewportI, CommandListener
{
- int startRes;
-
- int endRes;
-
- int startSeq;
-
- int endSeq;
-
Font font;
NJTree currentTree = null;
return sq;
}
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getStartRes()
- {
- return startRes;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getEndRes()
- {
- return endRes;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getStartSeq()
- {
- return startSeq;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param res
- * DOCUMENT ME!
- */
- public void setStartRes(int res)
- {
- this.startRes = res;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param seq
- * DOCUMENT ME!
- */
- public void setStartSeq(int seq)
- {
- this.startSeq = seq;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param res
- * DOCUMENT ME!
- */
- public void setEndRes(int res)
- {
- if (res > (alignment.getWidth() - 1))
- {
- // log.System.out.println(" Corrected res from " + res + " to maximum " +
- // (alignment.getWidth()-1));
- res = alignment.getWidth() - 1;
- }
-
- if (res < 0)
- {
- res = 0;
- }
-
- this.endRes = res;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param seq
- * DOCUMENT ME!
- */
- public void setEndSeq(int seq)
- {
- if (seq > alignment.getHeight())
- {
- seq = alignment.getHeight();
- }
-
- if (seq < 0)
- {
- seq = 0;
- }
-
- this.endSeq = seq;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getEndSeq()
- {
- return endSeq;
- }
-
boolean validCharWidth;
/**
return false;
}
- /**
- * when set, view will scroll to show the highlighted position
- */
- public boolean followHighlight = true;
-
- /**
- * @return true if view should scroll to show the highlighted region of a
- * sequence
- * @return
- */
- public boolean getFollowHighlight()
- {
- return followHighlight;
- }
-
public boolean followSelection = true;
/**
/**
* If this viewport has a (Protein/cDNA) complement, then scroll the
* complementary alignment to match this one.
- *
- * @param horizontal
- * true for horizontal scroll event, false for vertical
*/
- public void scrollComplementaryAlignment(boolean horizontal)
+ public void scrollComplementaryAlignment()
{
/*
- * If no complement, or it is not following scrolling, do nothing.
+ * Populate a SearchResults object with the mapped location to scroll to. If
+ * there is no complement, or it is not following highlights, or no mapping
+ * is found, the result will be empty.
*/
- // TODO pull up followHighlight to AlignmentViewport/AlignViewportI
- final AlignViewport codingComplement = (AlignViewport) getCodingComplement();
- if (codingComplement == null || !codingComplement.followHighlight)
- {
- return;
- }
- boolean iAmProtein = !getAlignment().isNucleotide();
- AlignmentI proteinAlignment = iAmProtein ? getAlignment()
- : codingComplement.getAlignment();
- if (proteinAlignment == null)
+ SearchResults sr = new SearchResults();
+ int seqOffset = findComplementScrollTarget(sr);
+ if (!sr.isEmpty())
{
- return;
- }
- final Set<AlignedCodonFrame> mappings = proteinAlignment
- .getCodonFrames();
-
- /*
- * Heuristic: find the first mapped sequence (if any) with a non-gapped
- * residue in the middle column of the visible region. Scroll the
- * complementary alignment to line up the corresponding residue.
- */
- int seqOffset = 0;
- SequenceI sequence = null;
- int middleColumn = getStartRes() + (getEndRes() - getStartRes()) / 2;
- final HiddenSequences hiddenSequences = getAlignment()
- .getHiddenSequences();
- for (int seqNo = getStartSeq(); seqNo < getEndSeq(); seqNo++, seqOffset++)
- {
- sequence = getAlignment().getSequenceAt(seqNo);
- if (hiddenSequences != null && hiddenSequences.isHidden(sequence))
- {
- continue;
- }
- if (Comparison.isGap(sequence.getCharAt(middleColumn)))
- {
- continue;
- }
- List<AlignedCodonFrame> seqMappings = MappingUtils
- .findMappingsForSequence(sequence, mappings);
- if (!seqMappings.isEmpty())
- {
- break;
- }
- }
-
- if (sequence == null)
- {
- /*
- * No ungapped mapped sequence in middle column - do nothing
- */
- return;
+ // TODO would like next line without cast but needs more refactoring...
+ final AlignmentPanel complementPanel = ((AlignViewport) getCodingComplement()).getAlignPanel();
+ complementPanel.setFollowingComplementScroll(true);
+ complementPanel.scrollToCentre(sr, seqOffset);
}
- SearchResults sr = MappingUtils.buildSearchResults(sequence,
- sequence.findPosition(middleColumn), mappings);
- codingComplement.getAlignPanel().scrollAsComplement(sr, seqOffset,
- horizontal);
}
}
// TODO: properly locate search results in view when large numbers of hidden
// columns exist before highlighted region
// do we need to scroll the panel?
- // TODO: tons of nullpointereexceptions raised here.
+ // TODO: tons of nullpointerexceptions raised here.
if (results != null && results.getSize() > 0 && av != null
&& av.getAlignment() != null)
{
}
else
{
- av.scrollComplementaryAlignment(evt.getSource() == hscroll);
+ av.scrollComplementaryAlignment();
}
}
* 'to'; may be modified for sequence offset by this method
* @param seqOffset
* the number of visible sequences to show above the mapped region
- * @param horizontal
- * if true, horizontal scrolling, else vertical
*/
- public void scrollAsComplement(SearchResults sr, int seqOffset,
- boolean horizontal)
+ public void scrollToCentre(SearchResults sr, int seqOffset)
{
/*
* To avoid jumpy vertical scrolling (if some sequences are gapped or not
.setSequence(av.getAlignment().getSequenceAt(sequenceIndex));
/*
- * Scroll to position but centring the target residue. Also set a state flag
- * to prevent adjustmentValueChanged performing this recursively.
+ * Scroll to position but centring the target residue.
*/
- setFollowingComplementScroll(true);
scrollToPosition(sr, true, true);
}
import jalview.io.SequenceAnnotationReport;
import jalview.util.MessageManager;
import jalview.util.UrlLink;
+import jalview.viewmodel.AlignmentViewport;
import java.awt.BorderLayout;
import java.awt.event.MouseEvent;
{
private IdCanvas idCanvas;
- protected AlignViewport av;
+ protected AlignmentViewport av;
protected AlignmentPanel alignPanel;
view.setShowGroupConservation(av.isShowGroupConservation());
view.setShowNPfeatureTooltip(av.isShowNPFeats());
view.setShowDbRefTooltip(av.isShowDBRefs());
- view.setFollowHighlight(av.followHighlight);
+ view.setFollowHighlight(av.isFollowHighlight());
view.setFollowSelection(av.followSelection);
view.setIgnoreGapsinConsensus(av.isIgnoreGapsConsensus());
if (av.getFeaturesDisplayed() != null)
}
if (view.hasFollowHighlight())
{
- af.viewport.followHighlight = view.getFollowHighlight();
+ af.viewport.setFollowHighlight(view.getFollowHighlight());
}
if (view.hasFollowSelection())
{
*/
package jalview.gui;
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Point;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.awt.event.MouseWheelEvent;
+import java.awt.event.MouseWheelListener;
+import java.util.List;
+import java.util.Vector;
+
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.ToolTipManager;
+
import jalview.api.AlignViewportI;
import jalview.commands.EditCommand;
import jalview.commands.EditCommand.Action;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
-import java.awt.BorderLayout;
-import java.awt.Color;
-import java.awt.Font;
-import java.awt.FontMetrics;
-import java.awt.Point;
-import java.awt.event.MouseEvent;
-import java.awt.event.MouseListener;
-import java.awt.event.MouseMotionListener;
-import java.awt.event.MouseWheelEvent;
-import java.awt.event.MouseWheelListener;
-import java.util.List;
-import java.util.Vector;
-
-import javax.swing.JOptionPane;
-import javax.swing.JPanel;
-import javax.swing.ToolTipManager;
-
/**
* DOCUMENT ME!
*
@Override
public void highlightSequence(SearchResults results)
{
- if (av.followHighlight)
+ if (av.isFollowHighlight())
{
if (ap.scrollToPosition(results, false))
{
public static SearchResults buildSearchResults(SequenceI seq, int index,
Set<AlignedCodonFrame> seqmappings)
{
- SearchResults results;
- results = new SearchResults();
+ SearchResults results = new SearchResults();
+ addSearchResults(results, seq, index, seqmappings);
+ return results;
+ }
+
+ /**
+ * Adds entries to a SearchResults object describing the mapped region
+ * corresponding to the specified sequence position.
+ *
+ * @param results
+ * @param seq
+ * @param index
+ * @param seqmappings
+ */
+ public static void addSearchResults(SearchResults results, SequenceI seq,
+ int index, Set<AlignedCodonFrame> seqmappings)
+ {
if (index >= seq.getStart() && index <= seq.getEnd())
{
for (AlignedCodonFrame acf : seqmappings)
acf.markMappedRegion(seq, index, results);
}
}
- return results;
}
/**
import jalview.datamodel.Annotation;
import jalview.datamodel.CigarArray;
import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenSequences;
+import jalview.datamodel.SearchResults;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceGroup;
import jalview.structure.CommandListener;
import jalview.structure.StructureSelectionManager;
import jalview.structure.VamsasSource;
+import jalview.util.Comparison;
+import jalview.util.MappingUtils;
import jalview.viewmodel.styles.ViewStyle;
import jalview.workers.AlignCalcManager;
import jalview.workers.ComplementConsensusThread;
protected boolean showAutocalculatedAbove;
/**
+ * when set, view will scroll to show the highlighted position
+ */
+ private boolean followHighlight = true;
+
+ // TODO private with getters and setters?
+ public int startRes;
+
+ public int endRes;
+
+ public int startSeq;
+
+ public int endSeq;
+
+ /**
* Property change listener for changes in alignment
*
* @param listener
{
viewStyle.setScaleProteinAsCdna(b);
}
+
+ /**
+ * @return true if view should scroll to show the highlighted region of a
+ * sequence
+ * @return
+ */
+ @Override
+ public final boolean isFollowHighlight()
+ {
+ return followHighlight;
+ }
+
+ @Override
+ public final void setFollowHighlight(boolean b)
+ {
+ this.followHighlight = b;
+ }
+
+ public int getStartRes()
+ {
+ return startRes;
+ }
+
+ public int getEndRes()
+ {
+ return endRes;
+ }
+
+ public int getStartSeq()
+ {
+ return startSeq;
+ }
+
+ public void setStartRes(int res)
+ {
+ this.startRes = res;
+ }
+
+ public void setStartSeq(int seq)
+ {
+ this.startSeq = seq;
+ }
+
+ public void setEndRes(int res)
+ {
+ if (res > alignment.getWidth() - 1)
+ {
+ // log.System.out.println(" Corrected res from " + res + " to maximum " +
+ // (alignment.getWidth()-1));
+ res = alignment.getWidth() - 1;
+ }
+ if (res < 0)
+ {
+ res = 0;
+ }
+ this.endRes = res;
+ }
+
+ public void setEndSeq(int seq)
+ {
+ if (seq > alignment.getHeight())
+ {
+ seq = alignment.getHeight();
+ }
+ if (seq < 0)
+ {
+ seq = 0;
+ }
+ this.endSeq = seq;
+ }
+
+ public int getEndSeq()
+ {
+ return endSeq;
+ }
+
+ /**
+ * Helper method to populate the SearchResults with the location in the
+ * complementary alignment to scroll to, in order to match this one.
+ *
+ * @param sr
+ * the SearchResults to add to
+ * @return the offset (below top of visible region) of the matched sequence
+ */
+ protected int findComplementScrollTarget(SearchResults sr)
+ {
+ final AlignViewportI codingComplement = getCodingComplement();
+ if (codingComplement == null || !codingComplement.isFollowHighlight())
+ {
+ return 0;
+ }
+ boolean iAmProtein = !getAlignment().isNucleotide();
+ AlignmentI proteinAlignment = iAmProtein ? getAlignment()
+ : codingComplement.getAlignment();
+ if (proteinAlignment == null)
+ {
+ return 0;
+ }
+ final Set<AlignedCodonFrame> mappings = proteinAlignment
+ .getCodonFrames();
+
+ /*
+ * Heuristic: find the first mapped sequence (if any) with a non-gapped
+ * residue in the middle column of the visible region. Scroll the
+ * complementary alignment to line up the corresponding residue.
+ */
+ int seqOffset = 0;
+ SequenceI sequence = null;
+ int middleColumn = getStartRes() + (getEndRes() - getStartRes()) / 2;
+ final HiddenSequences hiddenSequences = getAlignment()
+ .getHiddenSequences();
+ for (int seqNo = getStartSeq(); seqNo < getEndSeq(); seqNo++, seqOffset++)
+ {
+ sequence = getAlignment().getSequenceAt(seqNo);
+ if (hiddenSequences != null && hiddenSequences.isHidden(sequence))
+ {
+ continue;
+ }
+ if (Comparison.isGap(sequence.getCharAt(middleColumn)))
+ {
+ continue;
+ }
+ List<AlignedCodonFrame> seqMappings = MappingUtils
+ .findMappingsForSequence(sequence, mappings);
+ if (!seqMappings.isEmpty())
+ {
+ break;
+ }
+ }
+
+ if (sequence == null)
+ {
+ /*
+ * No ungapped mapped sequence in middle column - do nothing
+ */
+ return 0;
+ }
+ MappingUtils.addSearchResults(sr, sequence,
+ sequence.findPosition(middleColumn), mappings);
+ return seqOffset;
+ }
}
git://source.jalview.org / jalview.git / commitdiff