X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=4c662147d4304f42463603aa95332cf0aa1fa0fb;hb=20dd6fc13a9d903dc580939e7f2722bc9b043c4f;hp=c7ef3cedf42543f8d9cbed9235a6ebd7c97b18b6;hpb=ed2283c5f54da377a2a2fdbdb7aec75ed7041714;p=jalview.git diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java index c7ef3ce..4c66214 100644 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -20,6 +20,24 @@ */ 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.io.HTMLOutput; +import jalview.jbgui.GAlignmentPanel; +import jalview.math.AlignmentDimension; +import jalview.schemes.ResidueProperties; +import jalview.structure.StructureSelectionManager; +import jalview.util.ImageMaker; +import jalview.util.MessageManager; +import jalview.util.Platform; + import java.awt.BorderLayout; import java.awt.Color; import java.awt.Container; @@ -27,6 +45,7 @@ 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; @@ -41,21 +60,6 @@ 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! * @@ -304,7 +308,7 @@ public class AlignmentPanel extends GAlignmentPanel implements */ public boolean scrollToPosition(SearchResults results) { - return scrollToPosition(results, true, false); + return scrollToPosition(results, 0, true, false); } /** @@ -317,7 +321,7 @@ public class AlignmentPanel extends GAlignmentPanel implements */ public boolean scrollToPosition(SearchResults searchResults, boolean redrawOverview) { - return scrollToPosition(searchResults, redrawOverview, false); + return scrollToPosition(searchResults, 0, redrawOverview, false); } /** @@ -325,6 +329,9 @@ public class AlignmentPanel extends GAlignmentPanel implements * (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 @@ -332,6 +339,7 @@ public class AlignmentPanel extends GAlignmentPanel implements * @return false if results were not found */ public boolean scrollToPosition(SearchResults results, + int verticalOffset, boolean redrawOverview, boolean centre) { int startv, endv, starts, ends; @@ -390,6 +398,12 @@ public class AlignmentPanel extends GAlignmentPanel implements } } } + + /* + * 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) @@ -397,14 +411,16 @@ public class AlignmentPanel extends GAlignmentPanel implements /* * Scroll left to make start of search results visible */ - setScrollValues(start - 1, seqIndex); + // setScrollValues(start - 1, seqIndex); // plus one residue + setScrollValues(start, seqIndex); } else if ((endv = av.getEndRes()) <= end) { /* * Scroll right to make end of search results visible */ - setScrollValues(startv + 1 + end - endv, seqIndex); + // setScrollValues(startv + 1 + end - endv, seqIndex); // plus one + setScrollValues(startv + end - endv, seqIndex); } else if ((starts = av.getStartSeq()) > seqIndex) { @@ -509,47 +525,47 @@ 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) - { - // if the alignment is too big then - // default is 0.5 split - height = alignFrame.getHeight() / 2; - } - else + int rowHeight = av.getCharHeight(); + int alignmentHeight = rowHeight * av.getAlignment().getHeight(); + + /* + * Estimate available height in the AlignFrame for alignment + + * annotations. Deduct an estimate for title bar, menu bar, scale panel, + * hscroll, status bar (as these are not laid out we can't inspect their + * actual heights). Insets gives frame borders. + */ + int stuff = Platform.isAMac() ? 80 : 100; + Insets insets = alignFrame.getInsets(); + int availableHeight = alignFrame.getHeight() - stuff - 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 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(); } @@ -1223,7 +1239,7 @@ public class AlignmentPanel extends GAlignmentPanel implements return idwidth.intValue() + 4; } - void makeAlignmentImage(jalview.util.ImageMaker.TYPE type, File file) + void makeAlignmentImage(ImageMaker.TYPE type, File file) { long progress = System.currentTimeMillis(); headless = (System.getProperty("java.awt.headless") != null && System @@ -1239,14 +1255,14 @@ public class AlignmentPanel extends GAlignmentPanel implements AlignmentDimension aDimension = getAlignmentDimension(); try { - jalview.util.ImageMaker im; + ImageMaker im; final String imageAction, imageTitle; - if (type == jalview.util.ImageMaker.TYPE.PNG) + if (type == ImageMaker.TYPE.PNG) { imageAction = "Create PNG image from alignment"; imageTitle = null; } - else if (type == jalview.util.ImageMaker.TYPE.EPS) + else if (type == ImageMaker.TYPE.EPS) { imageAction = "Create EPS file from alignment"; imageTitle = alignFrame.getTitle(); @@ -1257,7 +1273,7 @@ public class AlignmentPanel extends GAlignmentPanel implements imageTitle = alignFrame.getTitle(); } - im = new jalview.util.ImageMaker(this, type, imageAction, + im = new ImageMaker(this, type, imageAction, aDimension.getWidth(), aDimension.getHeight(), file, imageTitle); if (av.getWrapAlignment()) @@ -1343,7 +1359,7 @@ public class AlignmentPanel extends GAlignmentPanel implements */ public void makeEPS(File epsFile) { - makeAlignmentImage(jalview.util.ImageMaker.TYPE.EPS, epsFile); + makeAlignmentImage(ImageMaker.TYPE.EPS, epsFile); } /** @@ -1351,12 +1367,12 @@ public class AlignmentPanel extends GAlignmentPanel implements */ public void makePNG(File pngFile) { - makeAlignmentImage(jalview.util.ImageMaker.TYPE.PNG, pngFile); + makeAlignmentImage(ImageMaker.TYPE.PNG, pngFile); } public void makeSVG(File svgFile) { - makeAlignmentImage(jalview.util.ImageMaker.TYPE.SVG, svgFile); + makeAlignmentImage(ImageMaker.TYPE.SVG, svgFile); } public void makePNGImageMap(File imgMapFile, String imageName) { @@ -1376,7 +1392,7 @@ public class AlignmentPanel extends GAlignmentPanel implements .getAlignment().getWidth(), g, gSize, f, fSize, sy; StringBuffer text = new StringBuffer(); PrintWriter out = new PrintWriter(new FileWriter(imgMapFile)); - out.println(jalview.io.HTMLOutput.getImageMapHTML()); + out.println(HTMLOutput.getImageMapHTML()); out.println("" + ""); @@ -1552,7 +1568,7 @@ public class AlignmentPanel extends GAlignmentPanel implements PaintRefresher.RemoveComponent(this); if (av != null) { - jalview.structure.StructureSelectionManager ssm = av + StructureSelectionManager ssm = av .getStructureSelectionManager(); ssm.removeStructureViewerListener(getSeqPanel(), null); ssm.removeSelectionListener(getSeqPanel()); @@ -1614,11 +1630,17 @@ public class AlignmentPanel extends GAlignmentPanel implements { try { + if (alignFrame.getSplitViewContainer() != null) + { + /* + * bring enclosing SplitFrame to front first if there is one + */ + ((SplitFrame) alignFrame.getSplitViewContainer()).setSelected(b); + } alignFrame.setSelected(b); } catch (Exception ex) { } - ; if (b) { @@ -1719,10 +1741,10 @@ public class AlignmentPanel extends GAlignmentPanel implements * @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 + * @param verticalOffset * the number of visible sequences to show above the mapped region */ - public void scrollToCentre(SearchResults sr, int seqOffset) + public void scrollToCentre(SearchResults sr, int verticalOffset) { /* * To avoid jumpy vertical scrolling (if some sequences are gapped or not @@ -1736,7 +1758,6 @@ public class AlignmentPanel extends GAlignmentPanel implements * 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) { @@ -1745,20 +1766,16 @@ public class AlignmentPanel extends GAlignmentPanel implements 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. */ - scrollToPosition(sr, true, true); + scrollToPosition(sr, verticalOffset, true, true); } /**