X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=2caea17d01aabf8bb9af9bd7c6d5935f0486412e;hb=HEAD;hp=454a73051a77a8330cb266217aae401a950931b7;hpb=230b5de09eda879e9b6078faacecc6d1f7659f35;p=jalview.git diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java index 454a730..845004b 100644 --- a/src/jalview/gui/SeqPanel.java +++ b/src/jalview/gui/SeqPanel.java @@ -44,7 +44,7 @@ import javax.swing.Timer; import javax.swing.ToolTipManager; import jalview.api.AlignViewportI; -import jalview.bin.Cache; +import jalview.bin.Console; import jalview.commands.EditCommand; import jalview.commands.EditCommand.Action; import jalview.commands.EditCommand.Edit; @@ -137,7 +137,7 @@ public class SeqPanel extends JPanel MousePos o = (MousePos) obj; boolean b = (column == o.column && seqIndex == o.seqIndex && annotationIndex == o.annotationIndex); - // System.out.println(obj + (b ? "= " : "!= ") + this); + // jalview.bin.Console.outPrintln(obj + (b ? "= " : "!= ") + this); return b; } @@ -246,8 +246,7 @@ public class SeqPanel extends JPanel ToolTipManager.sharedInstance().registerComponent(this); ToolTipManager.sharedInstance().setInitialDelay(0); ToolTipManager.sharedInstance().setDismissDelay(10000); - - + this.av = viewport; setBackground(Color.white); @@ -342,6 +341,16 @@ public class SeqPanel extends JPanel return new MousePos(col, seqIndex, annIndex); } + + /** + * @param evt + * @return absolute column in alignment nearest to the mouse pointer + */ + int findAlignmentColumn(MouseEvent evt) + { + return findNearestColumn(evt, true); + } + /** * Returns the aligned sequence position (base 0) at the mouse position, or * the closest visible one @@ -354,6 +363,17 @@ public class SeqPanel extends JPanel */ int findColumn(MouseEvent evt) { + return findNearestColumn(evt, false); + } + + /** + * @param nearestColumn + * when false returns negative values for out of bound positions - -1 + * for scale left/right, <-1 if far to right + * @return nearest absolute column to mouse pointer + */ + private int findNearestColumn(MouseEvent evt, boolean nearestColumn) + { int res = 0; int x = evt.getX(); @@ -377,7 +397,14 @@ public class SeqPanel extends JPanel if (x < 0) { // mouse is over left scale - return -1; + if (!nearestColumn) + { + return -1; + } + else + { + x = 0; + } } int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth()); @@ -387,8 +414,15 @@ public class SeqPanel extends JPanel } if (x >= cwidth * charWidth) { - // mouse is over right scale - return -1; + if (!nearestColumn) + { + // mouse is over right scale + return -1; + } + else + { + x = cwidth * charWidth - 1; + } } wrappedBlock = y / cHeight; @@ -405,8 +439,14 @@ public class SeqPanel extends JPanel * rather than right-hand gutter */ x = Math.min(x, seqCanvas.getX() + seqCanvas.getWidth()); + if (nearestColumn) + { + x = Math.max(x, 0); + } + res = (x / charWidth) + startRes; res = Math.min(res, av.getRanges().getEndRes()); + } if (av.hasHiddenColumns()) @@ -483,8 +523,9 @@ public class SeqPanel extends JPanel void moveCursor(int dx, int dy) { - moveCursor(dx, dy,false); + moveCursor(dx, dy, false); } + void moveCursor(int dx, int dy, boolean nextWord) { HiddenColumns hidden = av.getAlignment().getHiddenColumns(); @@ -492,11 +533,13 @@ public class SeqPanel extends JPanel if (nextWord) { int maxWidth = av.getAlignment().getWidth(); - int maxHeight=av.getAlignment().getHeight(); - SequenceI seqAtRow = av.getAlignment().getSequenceAt(seqCanvas.cursorY); + 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; + boolean isGap = Comparison + .isGap(seqAtRow.getCharAt(seqCanvas.cursorX)); + int p = seqCanvas.cursorX, lastP, r = seqCanvas.cursorY, lastR; do { lastP = p; @@ -517,19 +560,23 @@ public class SeqPanel extends JPanel 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 { + seqCanvas.cursorX = p; + seqCanvas.cursorY = r; + } + else + { int maxWidth = av.getAlignment().getWidth(); - seqCanvas.cursorX = nextVisible(hidden, maxWidth, seqCanvas.cursorX, dx); + seqCanvas.cursorX = nextVisible(hidden, maxWidth, seqCanvas.cursorX, + dx); seqCanvas.cursorY += dy; } scrollToVisible(false); } - private int nextVisible(HiddenColumns hidden,int maxWidth, int original, int dx) + private int nextVisible(HiddenColumns hidden, int maxWidth, int original, + int dx) { - int newCursorX=original+dx; + int newCursorX = original + dx; if (av.hasHiddenColumns() && !hidden.isVisible(newCursorX)) { int visx = hidden.absoluteToVisibleColumn(newCursorX - dx); @@ -550,13 +597,13 @@ public class SeqPanel extends JPanel } } newCursorX = (newCursorX < 0) ? 0 : newCursorX; - if (newCursorX >= maxWidth - || !hidden.isVisible(newCursorX)) + if (newCursorX >= maxWidth || !hidden.isVisible(newCursorX)) { newCursorX = original; } return newCursorX; } + /** * Scroll to make the cursor visible in the viewport. * @@ -612,7 +659,7 @@ public class SeqPanel extends JPanel if (av.getAlignment().getHiddenColumns().isVisible(seqCanvas.cursorX)) { setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY), - seqCanvas.cursorX, seqCanvas.cursorY); + seqCanvas.cursorX, seqCanvas.cursorY); } if (repaintNeeded) @@ -621,7 +668,6 @@ public class SeqPanel extends JPanel } } - void setSelectionAreaAtCursor(boolean topLeft) { SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY); @@ -875,7 +921,7 @@ public class SeqPanel extends JPanel if (lastMessage == null || !lastMessage.equals(tmp)) { - // System.err.println("mouseOver Sequence: "+tmp); + // jalview.bin.Console.errPrintln("mouseOver Sequence: "+tmp); ssm.mouseOverSequence(sequence, index, pos, av); } lastMessage = tmp; @@ -960,8 +1006,7 @@ public class SeqPanel extends JPanel SequenceI seq = match.getSequence(); SequenceI ds = seq.getDatasetSequence() == null ? seq : seq.getDatasetSequence(); - MappedFeatures mf = fr2 - .findComplementFeaturesAtResidue(ds, pos); + MappedFeatures mf = fr2.findComplementFeaturesAtResidue(ds, pos); if (mf != null) { for (SequenceFeature sf : mf.features) @@ -1001,7 +1046,7 @@ public class SeqPanel extends JPanel @Override public void updateColours(SequenceI seq, int index) { - System.out.println("update the seqPanel colours"); + jalview.bin.Console.outPrintln("update the seqPanel colours"); // repaint(); } @@ -1104,9 +1149,8 @@ public class SeqPanel extends JPanel { List features = ap.getFeatureRenderer() .findFeaturesAtColumn(sequence, column + 1); - unshownFeatures = seqARep.appendFeatures(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 @@ -1124,8 +1168,8 @@ public class SeqPanel extends JPanel pos); if (mf != null) { - unshownFeatures += seqARep.appendFeatures(tooltipText, - pos, mf, fr2, MAX_TOOLTIP_LENGTH); + unshownFeatures += seqARep.appendFeatures(tooltipText, pos, mf, + fr2, MAX_TOOLTIP_LENGTH); } } } @@ -1153,8 +1197,7 @@ public class SeqPanel extends JPanel if (!textString.equals(lastTooltip)) { lastTooltip = textString; - lastFormattedTooltip = JvSwingUtils.wrapTooltip(true, - textString); + lastFormattedTooltip = JvSwingUtils.wrapTooltip(true, textString); setToolTipText(lastFormattedTooltip); } } @@ -1172,6 +1215,7 @@ public class SeqPanel extends JPanel final int column = pos.column; final int rowIndex = pos.annotationIndex; + // TODO - get yOffset for annotation, too if (column < 0 || !av.getWrapAlignment() || !av.isShowAnnotation() || rowIndex < 0) { @@ -1180,8 +1224,9 @@ public class SeqPanel extends JPanel AlignmentAnnotation[] anns = av.getAlignment().getAlignmentAnnotation(); String tooltip = AnnotationPanel.buildToolTip(anns[rowIndex], column, - anns); - if (!tooltip.equals(lastTooltip)) + anns, 0, av, ap); + if (tooltip == null ? tooltip != lastTooltip + : !tooltip.equals(lastTooltip)) { lastTooltip = tooltip; lastFormattedTooltip = tooltip == null ? null @@ -1190,7 +1235,7 @@ public class SeqPanel extends JPanel } String msg = AnnotationPanel.getStatusMessage(av.getAlignment(), column, - anns[rowIndex]); + anns[rowIndex], 0, av); ap.alignFrame.setStatus(msg); } @@ -1237,8 +1282,8 @@ public class SeqPanel extends JPanel tempTip.setTipText(lastFormattedTooltip); int tipWidth = (int) tempTip.getPreferredSize().getWidth(); - - // was x += (w - x < 200) ? -(w / 2) : 5; + + // was x += (w - x < 200) ? -(w / 2) : 5; x = (x + tipWidth < w ? x + 10 : w - tipWidth); Point p = new Point(x, y + av.getCharHeight()); // BH 2018 was - 20? @@ -1252,7 +1297,8 @@ public class SeqPanel extends JPanel * changed, so selective redraws can be applied (ie. only structures, only * overview, etc) */ - private boolean updateOverviewAndStructs = false; // TODO: refactor to avcontroller + private boolean updateOverviewAndStructs = false; // TODO: refactor to + // avcontroller /** * set if av.getSelectionGroup() refers to a group that is defined on the @@ -1314,8 +1360,7 @@ public class SeqPanel extends JPanel * Sequence number (if known), and sequence name. */ String seqno = seqIndex == -1 ? "" : " " + (seqIndex + 1); - text.append("Sequence").append(seqno).append(" ID: ") - .append(seqName); + text.append("Sequence").append(seqno).append(" ID: ").append(seqName); String residue = null; @@ -1574,12 +1619,12 @@ public class SeqPanel extends JPanel String label = null; if (groupEditing) { - message.append("Edit group:"); + message.append("Edit group:"); label = MessageManager.getString("action.edit_group"); } else { - message.append("Edit sequence: " + seq.getName()); + message.append("Edit sequence: " + seq.getName()); label = seq.getName(); if (label.length() > 10) { @@ -1771,8 +1816,7 @@ public class SeqPanel extends JPanel { for (int j = 0; j < startres - editLastRes; j++) { - if (!Comparison - .isGap(groupSeqs[g].getCharAt(fixedRight - j))) + if (!Comparison.isGap(groupSeqs[g].getCharAt(fixedRight - j))) { blank = false; break; @@ -2164,8 +2208,8 @@ public class SeqPanel extends JPanel * highlight the first feature at the position on the alignment */ SearchResultsI highlight = new SearchResults(); - highlight.addResult(sequence, features.get(0).getBegin(), features - .get(0).getEnd()); + highlight.addResult(sequence, features.get(0).getBegin(), + features.get(0).getEnd()); seqCanvas.highlightSearchResults(highlight, true); /* @@ -2177,32 +2221,85 @@ public class SeqPanel extends JPanel } } + /** + * Responds to a mouse wheel movement by scrolling the alignment + * + * Note that this method may also be fired by scrolling with a gesture on a + * trackpad. + */ @Override public void mouseWheelMoved(MouseWheelEvent e) { e.consume(); double wheelRotation = e.getPreciseWheelRotation(); + + /* + * scroll more for large (fast) mouse movements + */ + int size = 1 + (int) Math.abs(wheelRotation); + if (wheelRotation > 0) { if (e.isShiftDown()) { - av.getRanges().scrollRight(true); - + /* + * scroll right + * stop trying to scroll right when limit is reached (saves + * expensive calls to Alignment.getWidth()) + */ + while (size-- > 0 && !ap.isScrolledFullyRight()) + { + if (!av.getRanges().scrollRight(true)) + { + break; + } + } } else { - av.getRanges().scrollUp(false); + /* + * scroll down + */ + while (size-- > 0) + { + if (!av.getRanges().scrollUp(false)) + { + break; + } + } } } else if (wheelRotation < 0) { if (e.isShiftDown()) { - av.getRanges().scrollRight(false); + /* + * scroll left + */ + while (size-- > 0) + { + if (!av.getRanges().scrollRight(false)) + { + break; + } + } } else { - av.getRanges().scrollUp(true); + /* + * scroll up + */ + while (size-- > 0) + { + if (!av.getRanges().scrollUp(true)) + { + break; + } + } } } @@ -2429,7 +2526,7 @@ public class SeqPanel extends JPanel return; } - res = Math.min(res, av.getAlignment().getWidth()-1); + res = Math.min(res, av.getAlignment().getWidth() - 1); if (stretchGroup.getEndRes() == res) { @@ -2802,7 +2899,7 @@ public class SeqPanel extends JPanel { if (av.getAlignment() == null) { - Cache.log.warn("alignviewport av SeqSetId=" + av.getSequenceSetId() + Console.warn("alignviewport av SeqSetId=" + av.getSequenceSetId() + " ViewId=" + av.getViewId() + " 's alignment is NULL! returning immediately."); return; @@ -2857,7 +2954,7 @@ public class SeqPanel extends JPanel if (copycolsel && av.hasHiddenColumns() && (av.getAlignment().getHiddenColumns() == null)) { - System.err.println("Bad things"); + jalview.bin.Console.errPrintln("Bad things"); } if (repaint) // always true! { @@ -2927,6 +3024,8 @@ public class SeqPanel extends JPanel * if hidden column selection has changed */ ap.paintAlignment(hiddenChanged, hiddenChanged); + // propagate any selection changes + PaintRefresher.Refresh(ap, av.getSequenceSetId()); return true; }