X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=bb85948a7a2c9ece090e6414da9cbe7cd390ba81;hb=af259f508805faf2da90585ee9a67cd7853bf5aa;hp=08e11945428980d43b6c09617e78c1c953e0e5c0;hpb=81029aa176cd9a4553e297f7be95931dddc89974;p=jalview.git diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java index 08e1194..bb85948 100644 --- a/src/jalview/gui/SeqPanel.java +++ b/src/jalview/gui/SeqPanel.java @@ -20,6 +20,24 @@ */ 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.ArrayList; +import java.util.Collections; +import java.util.List; + +import javax.swing.JPanel; +import javax.swing.SwingUtilities; +import javax.swing.ToolTipManager; + import jalview.api.AlignViewportI; import jalview.bin.Cache; import jalview.commands.EditCommand; @@ -53,24 +71,6 @@ import jalview.viewmodel.AlignmentViewport; import jalview.viewmodel.ViewportRanges; import jalview.viewmodel.seqfeatures.FeatureRendererModel; -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.ArrayList; -import java.util.Collections; -import java.util.List; - -import javax.swing.JPanel; -import javax.swing.SwingUtilities; -import javax.swing.ToolTipManager; - /** * DOCUMENT ME! * @@ -207,8 +207,6 @@ public class SeqPanel extends JPanel StringBuffer keyboardNo2; - java.net.URL linkImageURL; - private final SequenceAnnotationReport seqARep; StringBuilder tooltipText = new StringBuilder(); @@ -229,8 +227,7 @@ public class SeqPanel extends JPanel */ public SeqPanel(AlignViewport viewport, AlignmentPanel alignPanel) { - linkImageURL = getClass().getResource("/images/link.gif"); - seqARep = new SequenceAnnotationReport(linkImageURL.toString()); + seqARep = new SequenceAnnotationReport(true); ToolTipManager.sharedInstance().registerComponent(this); ToolTipManager.sharedInstance().setInitialDelay(0); ToolTipManager.sharedInstance().setDismissDelay(10000); @@ -463,47 +460,80 @@ public class SeqPanel extends JPanel void moveCursor(int dx, int dy) { - seqCanvas.cursorX += dx; - seqCanvas.cursorY += dy; - + moveCursor(dx, dy,false); + } + void moveCursor(int dx, int dy, boolean nextWord) + { HiddenColumns hidden = av.getAlignment().getHiddenColumns(); - if (av.hasHiddenColumns() && !hidden.isVisible(seqCanvas.cursorX)) + if (nextWord) { - int original = seqCanvas.cursorX - dx; int maxWidth = av.getAlignment().getWidth(); - - if (!hidden.isVisible(seqCanvas.cursorX)) - { - int visx = hidden.absoluteToVisibleColumn(seqCanvas.cursorX - dx); - int[] region = hidden.getRegionWithEdgeAtRes(visx); - - if (region != null) // just in case + int maxHeight=av.getAlignment().getHeight(); + SequenceI seqAtRow = av.getAlignment().getSequenceAt(seqCanvas.cursorY); + // look for next gap or residue + boolean isGap = Comparison.isGap(seqAtRow.getCharAt(seqCanvas.cursorX)); + int p = seqCanvas.cursorX,lastP,r=seqCanvas.cursorY,lastR; + do + { + lastP = p; + lastR = r; + if (dy != 0) { - if (dx == 1) + r += dy; + if (r < 0) { - // moving right - seqCanvas.cursorX = region[1] + 1; + r = 0; } - else if (dx == -1) + if (r >= maxHeight) { - // moving left - seqCanvas.cursorX = region[0] - 1; + r = maxHeight - 1; } + seqAtRow = av.getAlignment().getSequenceAt(r); } - seqCanvas.cursorX = (seqCanvas.cursorX < 0) ? 0 : seqCanvas.cursorX; - } + p = nextVisible(hidden, maxWidth, p, dx); + } while ((dx != 0 ? p != lastP : r != lastR) + && isGap == Comparison.isGap(seqAtRow.getCharAt(p))); + seqCanvas.cursorX=p; + seqCanvas.cursorY=r; + } else { + int maxWidth = av.getAlignment().getWidth(); + seqCanvas.cursorX = nextVisible(hidden, maxWidth, seqCanvas.cursorX, dx); + seqCanvas.cursorY += dy; + } + scrollToVisible(false); + } + + private int nextVisible(HiddenColumns hidden,int maxWidth, int original, int dx) + { + int newCursorX=original+dx; + if (av.hasHiddenColumns() && !hidden.isVisible(newCursorX)) + { + int visx = hidden.absoluteToVisibleColumn(newCursorX - dx); + int[] region = hidden.getRegionWithEdgeAtRes(visx); - if (seqCanvas.cursorX >= maxWidth - || !hidden.isVisible(seqCanvas.cursorX)) + if (region != null) // just in case { - seqCanvas.cursorX = original; + if (dx == 1) + { + // moving right + newCursorX = region[1] + 1; + } + else if (dx == -1) + { + // moving left + newCursorX = region[0] - 1; + } } } - - scrollToVisible(false); + newCursorX = (newCursorX < 0) ? 0 : newCursorX; + if (newCursorX >= maxWidth + || !hidden.isVisible(newCursorX)) + { + newCursorX = original; + } + return newCursorX; } - /** * Scroll to make the cursor visible in the viewport. * @@ -865,7 +895,8 @@ public class SeqPanel extends JPanel { setStatusMessage(results); } - return results.isEmpty() ? null : getHighlightInfo(results); + // JAL-3303 feature suppressed for now pending review + return null; // results.isEmpty() ? null : getHighlightInfo(results); } /** @@ -895,11 +926,12 @@ public class SeqPanel extends JPanel AlignFrame af = Desktop.getAlignFrameFor(complement); FeatureRendererModel fr2 = af.getFeatureRenderer(); - int j = results.getSize(); + List matches = results.getResults(); + int j = matches.size(); List infos = new ArrayList<>(); for (int i = 0; i < j; i++) { - SearchResultMatchI match = results.getResults().get(i); + SearchResultMatchI match = matches.get(i); int pos = match.getStart(); if (pos == match.getEnd()) { @@ -1047,9 +1079,9 @@ public class SeqPanel extends JPanel { List features = ap.getFeatureRenderer() .findFeaturesAtColumn(sequence, column + 1); - unshownFeatures = seqARep.appendFeaturesLengthLimit(tooltipText, pos, - features, - this.ap.getSeqPanel().seqCanvas.fr, MAX_TOOLTIP_LENGTH); + unshownFeatures = seqARep.appendFeatures(tooltipText, pos, + features, this.ap.getSeqPanel().seqCanvas.fr, + MAX_TOOLTIP_LENGTH); /* * add features in CDS/protein complement at the corresponding @@ -1067,9 +1099,8 @@ public class SeqPanel extends JPanel pos); if (mf != null) { - unshownFeatures = seqARep.appendFeaturesLengthLimit( - tooltipText, pos, mf, fr2, - MAX_TOOLTIP_LENGTH); + unshownFeatures += seqARep.appendFeatures(tooltipText, + pos, mf, fr2, MAX_TOOLTIP_LENGTH); } } } @@ -1203,7 +1234,7 @@ public class SeqPanel extends JPanel { char sequenceChar = sequence.getCharAt(column); int pos = sequence.findPosition(column); - setStatusMessage(sequence, seqIndex, sequenceChar, pos); + setStatusMessage(sequence.getName(), seqIndex, sequenceChar, pos); return pos; } @@ -1219,7 +1250,7 @@ public class SeqPanel extends JPanel * Sequence 6 ID: O.niloticus.3 Nucleotide: Uracil (2) * * - * @param sequence + * @param seqName * @param seqIndex * sequence position in the alignment (1..) * @param sequenceChar @@ -1227,7 +1258,7 @@ public class SeqPanel extends JPanel * @param residuePos * the sequence residue position (if not over a gap) */ - protected void setStatusMessage(SequenceI sequence, int seqIndex, + protected void setStatusMessage(String seqName, int seqIndex, char sequenceChar, int residuePos) { StringBuilder text = new StringBuilder(32); @@ -1237,7 +1268,7 @@ public class SeqPanel extends JPanel */ String seqno = seqIndex == -1 ? "" : " " + (seqIndex + 1); text.append("Sequence").append(seqno).append(" ID: ") - .append(sequence.getName()); + .append(seqName); String residue = null; @@ -1282,7 +1313,8 @@ public class SeqPanel extends JPanel { return; } - SequenceI ds = al.getSequenceAt(sequenceIndex).getDatasetSequence(); + SequenceI alignedSeq = al.getSequenceAt(sequenceIndex); + SequenceI ds = alignedSeq.getDatasetSequence(); for (SearchResultMatchI m : results.getResults()) { SequenceI seq = m.getSequence(); @@ -1294,8 +1326,8 @@ public class SeqPanel extends JPanel if (seq == ds) { int start = m.getStart(); - setStatusMessage(seq, sequenceIndex, seq.getCharAt(start - 1), - start); + setStatusMessage(alignedSeq.getName(), sequenceIndex, + seq.getCharAt(start - 1), start); return; } } @@ -2060,7 +2092,7 @@ public class SeqPanel extends JPanel return; } - if (evt.getClickCount() > 1) + if (evt.getClickCount() > 1 && av.isShowSequenceFeatures()) { sg = av.getSelectionGroup(); if (sg != null && sg.getSize() == 1