X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=7228e1b20b0c5005afeea6d274c1515024633a7a;hb=59bcebdf52d535ff621840b2d836ecfc0f605ec1;hp=6c8046478c97860ece08ba02d753cf06a3f27aac;hpb=ffea8e06f34c1004671749a799722f64a83d8161;p=jalview.git diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java index 6c80464..7228e1b 100644 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -21,6 +21,7 @@ package jalview.gui; import jalview.analysis.AnnotationSorter; +import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; import jalview.bin.Cache; import jalview.datamodel.AlignmentI; @@ -41,6 +42,7 @@ import java.awt.Dimension; import java.awt.Font; import java.awt.FontMetrics; import java.awt.Graphics; +import java.awt.Insets; import java.awt.event.AdjustmentEvent; import java.awt.event.AdjustmentListener; import java.awt.print.PageFormat; @@ -51,6 +53,7 @@ import java.beans.PropertyChangeListener; import java.io.File; import java.io.FileWriter; import java.io.PrintWriter; +import java.util.List; import javax.swing.SwingUtilities; @@ -90,13 +93,17 @@ 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. * * @param af - * DOCUMENT ME! * @param av - * DOCUMENT ME! */ public AlignmentPanel(AlignFrame af, final AlignViewport av) { @@ -122,8 +129,6 @@ public class AlignmentPanel extends GAlignmentPanel implements setScrollValues(0, 0); - setAnnotationVisible(av.getShowAnnotation()); - hscroll.addAdjustmentListener(this); vscroll.addAdjustmentListener(this); @@ -141,9 +146,14 @@ public class AlignmentPanel extends GAlignmentPanel implements }); fontChanged(); adjustAnnotationHeight(); - + updateLayout(); } + @Override + public AlignViewportI getAlignViewport() + { + return av; + } public void alignmentChanged() { av.alignmentChanged(this); @@ -163,9 +173,10 @@ public class AlignmentPanel extends GAlignmentPanel implements // to prevent drawing old image FontMetrics fm = getFontMetrics(av.getFont()); - scalePanelHolder.setPreferredSize(new Dimension(10, av.charHeight + scalePanelHolder.setPreferredSize(new Dimension(10, av.getCharHeight() + fm.getDescent())); - idSpaceFillerPanel1.setPreferredSize(new Dimension(10, av.charHeight + idSpaceFillerPanel1.setPreferredSize(new Dimension(10, av + .getCharHeight() + fm.getDescent())); getIdPanel().getIdCanvas().gg = null; @@ -173,6 +184,7 @@ public class AlignmentPanel extends GAlignmentPanel implements getAnnotationPanel().adjustPanelHeight(); Dimension d = calculateIdWidth(); + d.setSize(d.width + 4, d.height); getIdPanel().getIdCanvas().setPreferredSize(d); hscrollFillerPanel.setPreferredSize(d); @@ -181,6 +193,10 @@ public class AlignmentPanel extends GAlignmentPanel implements { overviewPanel.setBoxPosition(); } + if (this.alignFrame.getSplitViewContainer() != null) + { + ((SplitFrame) this.alignFrame.getSplitViewContainer()).adjustLayout(); + } repaint(); } @@ -195,11 +211,21 @@ public class AlignmentPanel extends GAlignmentPanel implements public Dimension calculateIdWidth() { // calculate sensible default width when no preference is available - - int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300); - int maxwidth = Math.max(20, - Math.min(afwidth - 200, 2 * afwidth / 3)); - return calculateIdWidth(maxwidth); + Dimension r = null; + if (av.getIdWidth() < 0) + { + int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300); + int maxwidth = Math.max(20, Math.min(afwidth - 200, 2 * afwidth / 3)); + r = calculateIdWidth(maxwidth); + av.setIdWidth(r.width); + } + else + { + r = new Dimension(); + r.width = av.getIdWidth(); + r.height = 0; + } + return r; } /** @@ -272,33 +298,52 @@ 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, 0, true, false); + } + + /** + * 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, 0, redrawOverview, 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 results + * @param verticalOffset + * if greater than zero, allows scrolling to a position below the + * first displayed sequence * @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) + int verticalOffset, + 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? - // TODO: tons of nullpointereexceptions raised here. + // TODO: tons of nullpointerexceptions raised here. if (results != null && results.getSize() > 0 && av != null && av.getAlignment() != null) { @@ -318,6 +363,17 @@ 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; @@ -339,24 +395,47 @@ public class AlignmentPanel extends GAlignmentPanel implements } } } - if (!av.wrapAlignment) + + /* + * allow for offset of target sequence (actually scroll to one above it) + */ + seqIndex = Math.max(0, seqIndex - verticalOffset); + + if (!av.getWrapAlignment()) { if ((startv = av.getStartRes()) >= start) { - setScrollValues(start - 1, seqIndex); + /* + * Scroll left to make start of search results visible + */ + // setScrollValues(start - 1, seqIndex); // plus one residue + setScrollValues(start, seqIndex); } else if ((endv = av.getEndRes()) <= end) { - setScrollValues(startv + 1 + end - endv, seqIndex); + /* + * Scroll right to make end of search results visible + */ + // setScrollValues(startv + 1 + end - endv, seqIndex); // plus one + setScrollValues(startv + 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 { @@ -412,7 +491,7 @@ public class AlignmentPanel extends GAlignmentPanel implements */ public void setAnnotationVisible(boolean b) { - if (!av.wrapAlignment) + if (!av.getWrapAlignment()) { annotationSpaceFillerHolder.setVisible(b); annotationScroller.setVisible(b); @@ -443,58 +522,60 @@ public class AlignmentPanel extends GAlignmentPanel implements */ protected void validateAnnotationDimensions(boolean adjustPanelHeight) { - int height = getAnnotationPanel().adjustPanelHeight(); - - int theight = av.getCharHeight() - * (av.getAlignment().getHeight() + (!av.hasHiddenRows() ? 0 - : av.getAlignment().getHiddenSequences().getSize())); - float sscaling = (float) (theight / (1.0 * theight + height)); - float ascaling = (float) (height * 1.0 / alignFrame.getHeight()); - int rheight = alignFrame.getHeight() - height - av.getCharHeight(); + int annotationHeight = getAnnotationPanel().adjustPanelHeight(); + if (adjustPanelHeight) { - // NOTE: this logic is different in the applet. Need a better algorithm to - // define behaviour - // try and set height according to alignment - if (ascaling > 0 && sscaling < 0.5) + int rowHeight = av.getCharHeight(); + int alignmentHeight = rowHeight * av.getAlignment().getHeight(); + + /* + * Estimate available height in the AlignFrame for alignment + + * annotations. Deduct an estimate of 75 for menu bar, scale panel, + * hscroll, status bar (as these are not laid out we can't inspect their + * actual heights). Insets gives borders including title bar. + */ + Insets insets = alignFrame.getInsets(); + int availableHeight = alignFrame.getHeight() - 75 - insets.top + - insets.bottom; + + /* + * If not enough vertical space, maximize annotation height while keeping + * at least two rows of alignment visible + */ + if (annotationHeight + alignmentHeight > availableHeight) { - // if the alignment is too big then - // default is 0.5 split - height = alignFrame.getHeight() / 2; - } - else - { - // if space for more than one sequence row left when annotation is fully - // displayed then set height to annotation height - // otherwise, leave at least two lines of sequence shown. - height = (rheight > av.getCharHeight()) ? height - : (-av.getCharHeight() * 3 + (int) (alignFrame.getHeight() * (1 - sscaling))); + annotationHeight = Math.min(annotationHeight, availableHeight - 2 + * rowHeight); } } else { // maintain same window layout whilst updating sliders - height = annotationScroller.getSize().height; + annotationHeight = annotationScroller.getSize().height; } hscroll.addNotify(); annotationScroller.setPreferredSize(new Dimension(annotationScroller - .getWidth(), height)); + .getWidth(), annotationHeight)); annotationSpaceFillerHolder.setPreferredSize(new Dimension( - annotationSpaceFillerHolder.getWidth(), height)); - annotationScroller.validate();// repaint(); + annotationSpaceFillerHolder.getWidth(), annotationHeight)); + annotationScroller.validate(); annotationScroller.addNotify(); } /** - * DOCUMENT ME! + * update alignment layout for viewport settings * * @param wrap * DOCUMENT ME! */ - public void setWrapAlignment(boolean wrap) + public void updateLayout() { + fontChanged(); + setAnnotationVisible(av.isShowAnnotation()); + boolean wrap = av.getWrapAlignment(); av.startSeq = 0; scalePanelHolder.setVisible(!wrap); hscroll.setVisible(!wrap); @@ -605,10 +686,11 @@ public class AlignmentPanel extends GAlignmentPanel implements width = av.getColumnSelection().findColumnPosition(width); } - av.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av.charWidth)) - 1); + av.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av + .getCharWidth())) - 1); - hextent = getSeqPanel().seqCanvas.getWidth() / av.charWidth; - vextent = getSeqPanel().seqCanvas.getHeight() / av.charHeight; + hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth(); + vextent = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight(); if (hextent > width) { @@ -652,7 +734,6 @@ public class AlignmentPanel extends GAlignmentPanel implements */ public void adjustmentValueChanged(AdjustmentEvent evt) { - int oldX = av.getStartRes(); int oldY = av.getStartSeq(); @@ -729,12 +810,24 @@ public class AlignmentPanel extends GAlignmentPanel implements getSeqPanel().seqCanvas.fastPaint(scrollX, scrollY); getScalePanel().repaint(); - if (av.getShowAnnotation() && scrollX != 0) + if (av.isShowAnnotation() && scrollX != 0) { getAnnotationPanel().fastPaint(scrollX); } } } + /* + * 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(); + } } /** @@ -859,7 +952,7 @@ public class AlignmentPanel extends GAlignmentPanel implements { int idWidth = getVisibleIdWidth(false); FontMetrics fm = getFontMetrics(av.getFont()); - int scaleHeight = av.charHeight + fm.getDescent(); + int scaleHeight = av.getCharHeight() + fm.getDescent(); pg.setColor(Color.white); pg.fillRect(0, 0, pwidth, pheight); @@ -949,7 +1042,7 @@ public class AlignmentPanel extends GAlignmentPanel implements } pg.setColor(currentColor); - pg.fillRect(0, (i - startSeq) * av.charHeight, idWidth, + pg.fillRect(0, (i - startSeq) * av.getCharHeight(), idWidth, av.getCharHeight()); pg.setColor(currentTextColor); @@ -966,7 +1059,7 @@ public class AlignmentPanel extends GAlignmentPanel implements pg.drawString( seq.getDisplayId(av.getShowJVSuffix()), xPos, - (((i - startSeq) * av.charHeight) + av.getCharHeight()) + (((i - startSeq) * av.getCharHeight()) + av.getCharHeight()) - (av.getCharHeight() / 5)); } @@ -981,7 +1074,8 @@ public class AlignmentPanel extends GAlignmentPanel implements // draw annotation - need to offset for current scroll position int offset = -getAlabels().getScrollOffset(); pg.translate(0, offset); - pg.translate(-idWidth - 3, (endSeq - startSeq) * av.charHeight + 3); + pg.translate(-idWidth - 3, (endSeq - startSeq) * av.getCharHeight() + + 3); getAlabels().drawComponent(pg, idWidth); pg.translate(idWidth + 3, 0); getAnnotationPanel().renderer.drawComponent(getAnnotationPanel(), av, @@ -1012,7 +1106,6 @@ public class AlignmentPanel extends GAlignmentPanel implements public int printWrappedAlignment(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException { - int annotationHeight = 0; AnnotationLabels labels = null; if (av.isShowAnnotation()) @@ -1021,13 +1114,13 @@ public class AlignmentPanel extends GAlignmentPanel implements labels = new AnnotationLabels(av); } - int hgap = av.charHeight; - if (av.scaleAboveWrapped) + int hgap = av.getCharHeight(); + if (av.getScaleAboveWrapped()) { - hgap += av.charHeight; + hgap += av.getCharHeight(); } - int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap + int cHeight = av.getAlignment().getHeight() * av.getCharHeight() + hgap + annotationHeight; int idWidth = getVisibleIdWidth(false); @@ -1071,18 +1164,19 @@ public class AlignmentPanel extends GAlignmentPanel implements xPos = idWidth - fm.stringWidth(string) - 4; } pg.drawString(string, xPos, - ((i * av.charHeight) + ypos + av.charHeight) - - (av.charHeight / 5)); + ((i * av.getCharHeight()) + ypos + av.getCharHeight()) + - (av.getCharHeight() / 5)); } if (labels != null) { pg.translate(-3, ypos - + (av.getAlignment().getHeight() * av.charHeight)); + + (av.getAlignment().getHeight() * av.getCharHeight())); pg.setFont(av.getFont()); labels.drawComponent(pg, idWidth); pg.translate(+3, -ypos - - (av.getAlignment().getHeight() * av.charHeight)); + - (av.getAlignment().getHeight() * av + .getCharHeight())); } ypos += cHeight; @@ -1149,8 +1243,7 @@ public class AlignmentPanel extends GAlignmentPanel implements if (alignFrame != null && !headless) { alignFrame.setProgressBar(MessageManager.formatMessage( - "status.saving_file", - new String[] + "status.saving_file", new Object[] { type.getLabel() }), progress); } try @@ -1225,9 +1318,9 @@ public class AlignmentPanel extends GAlignmentPanel implements maxwidth = av.getColumnSelection().findColumnPosition(maxwidth); } - int height = ((av.getAlignment().getHeight() + 1) * av.charHeight) + int height = ((av.getAlignment().getHeight() + 1) * av.getCharHeight()) + getScalePanel().getHeight(); - int width = getVisibleIdWidth(false) + (maxwidth * av.charWidth); + int width = getVisibleIdWidth(false) + (maxwidth * av.getCharWidth()); if (av.getWrapAlignment()) { @@ -1249,7 +1342,7 @@ public class AlignmentPanel extends GAlignmentPanel implements } } - else if (av.getShowAnnotation()) + else if (av.isShowAnnotation()) { height += getAnnotationPanel().adjustPanelHeight() + 3; } @@ -1283,7 +1376,7 @@ public class AlignmentPanel extends GAlignmentPanel implements // //////////////////////////////////////////// int idWidth = getVisibleIdWidth(false); FontMetrics fm = getFontMetrics(av.getFont()); - int scaleHeight = av.charHeight + fm.getDescent(); + int scaleHeight = av.getCharHeight() + fm.getDescent(); // Gen image map // //////////////////////////////// @@ -1302,33 +1395,32 @@ public class AlignmentPanel extends GAlignmentPanel implements for (s = 0; s < sSize; s++) { - sy = s * av.charHeight + scaleHeight; + sy = s * av.getCharHeight() + scaleHeight; SequenceI seq = av.getAlignment().getSequenceAt(s); - SequenceFeature[] features = seq.getDatasetSequence() - .getSequenceFeatures(); + SequenceFeature[] features = seq.getSequenceFeatures(); SequenceGroup[] groups = av.getAlignment().findAllGroups(seq); for (res = 0; res < alwidth; res++) { text = new StringBuffer(); - Object obj = null; + String triplet = null; if (av.getAlignment().isNucleotide()) { - obj = ResidueProperties.nucleotideName.get(seq.getCharAt(res) + triplet = ResidueProperties.nucleotideName.get(seq + .getCharAt(res) + ""); } else { - obj = ResidueProperties.aa2Triplet.get(seq.getCharAt(res) + triplet = ResidueProperties.aa2Triplet.get(seq.getCharAt(res) + ""); } - if (obj == null) + if (triplet == null) { continue; } - String triplet = obj.toString(); int alIndex = seq.findPosition(res); gSize = groups.length; for (g = 0; g < gSize; g++) @@ -1336,9 +1428,10 @@ public class AlignmentPanel extends GAlignmentPanel implements if (text.length() < 1) { text.append(" seqs = av.getAlignment().getSequences(); + + /* + * This is like AlignmentI.findIndex(seq) but here we are matching the + * dataset sequence not the aligned sequence + */ + boolean matched = false; + for (SequenceI seq : seqs) + { + if (mappedTo == seq.getDatasetSequence()) + { + matched = true; + break; + } + } + if (!matched) + { + return; // failsafe, shouldn't happen + } + + /* + * Scroll to position but centring the target residue. + */ + scrollToPosition(sr, verticalOffset, 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; + } }