X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;fp=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=851c58b8ccb3e5fef4accf80290a8d50e7957ad6;hb=9612728299dc4c2242a6a968875a194624983920;hp=beafa8cb36ed9b916ef9fc2e185f519ef475be46;hpb=71881f2cf715e6143cd594e20bd41db538282f81;p=jalview.git diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java index beafa8c..851c58b 100644 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -20,21 +20,6 @@ */ package jalview.gui; -import jalview.analysis.AnnotationSorter; -import jalview.api.AlignViewportI; -import jalview.api.AlignmentViewPanel; -import jalview.bin.Cache; -import jalview.datamodel.AlignmentI; -import jalview.datamodel.SearchResults; -import jalview.datamodel.SequenceFeature; -import jalview.datamodel.SequenceGroup; -import jalview.datamodel.SequenceI; -import jalview.jbgui.GAlignmentPanel; -import jalview.math.AlignmentDimension; -import jalview.schemes.ResidueProperties; -import jalview.structure.StructureSelectionManager; -import jalview.util.MessageManager; - import java.awt.BorderLayout; import java.awt.Color; import java.awt.Container; @@ -52,9 +37,25 @@ import java.beans.PropertyChangeListener; import java.io.File; import java.io.FileWriter; import java.io.PrintWriter; +import java.util.List; import javax.swing.SwingUtilities; +import jalview.analysis.AnnotationSorter; +import jalview.api.AlignViewportI; +import jalview.api.AlignmentViewPanel; +import jalview.bin.Cache; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.SearchResults; +import jalview.datamodel.SequenceFeature; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; +import jalview.jbgui.GAlignmentPanel; +import jalview.math.AlignmentDimension; +import jalview.schemes.ResidueProperties; +import jalview.structure.StructureSelectionManager; +import jalview.util.MessageManager; + /** * DOCUMENT ME! * @@ -91,6 +92,12 @@ public class AlignmentPanel extends GAlignmentPanel implements int vextent = 0; + /* + * Flag set while scrolling to follow complementary cDNA/protein scroll. When + * true, suppresses invoking the same method recursively. + */ + private boolean followingComplementScroll; + /** * Creates a new AlignmentPanel object. * @@ -290,29 +297,44 @@ public class AlignmentPanel extends GAlignmentPanel implements } /** - * scroll the view to show the position of the highlighted region in results + * Scroll the view to show the position of the highlighted region in results * (if any) and redraw the overview * * @param results */ public boolean scrollToPosition(SearchResults results) { - return scrollToPosition(results, true); + return scrollToPosition(results, true, false); } /** - * scroll the view to show the position of the highlighted region in results + * Scroll the view to show the position of the highlighted region in results + * (if any) + * + * @param searchResults + * @param redrawOverview + * @return + */ + public boolean scrollToPosition(SearchResults searchResults, boolean redrawOverview) + { + return scrollToPosition(searchResults, 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) + * @param centre + * if true, try to centre the search results horizontally in the view * @return false if results were not found */ public boolean scrollToPosition(SearchResults results, - boolean redrawOverview) + boolean redrawOverview, boolean centre) { - int startv, endv, starts, ends, width; + int startv, endv, starts, ends; // TODO: properly locate search results in view when large numbers of hidden // columns exist before highlighted region // do we need to scroll the panel? @@ -336,6 +358,17 @@ public class AlignmentPanel extends GAlignmentPanel implements int end = r[1]; // System.err.println("Seq : "+seqIndex+" Scroll to "+start+","+end); // // DEBUG + + /* + * 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; @@ -361,20 +394,35 @@ public class AlignmentPanel extends GAlignmentPanel implements { 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); } else if ((ends = av.getEndSeq()) <= seqIndex) { + /* + * Scroll down to make end of search results visible + */ setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1); } + /* + * Else results are already visible - no need to scroll + */ } else { @@ -756,6 +804,18 @@ public class AlignmentPanel extends GAlignmentPanel implements } } } + /* + * If there is one, scroll the (Protein/cDNA) complementary alignment to + * match, unless we are ourselves doing that. + */ + if (isFollowingComplementScroll()) + { + setFollowingComplementScroll(false); + } + else + { + av.scrollComplementaryAlignment(evt.getSource() == hscroll); + } } /** @@ -1651,4 +1711,73 @@ public class AlignmentPanel extends GAlignmentPanel implements { this.idPanel = idPanel; } + + /** + * 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 + * @param horizontal + * if true, horizontal scrolling, else vertical + */ + public void scrollAsComplement(SearchResults sr, int seqOffset, + boolean horizontal) + { + /* + * 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 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); + } + + /** + * 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; + } }