X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=3dfb5105fcaf77d7c3312e8b0468d3bc5af44d09;hb=bf478b2e1087fb03bf6b9fb07f14a9e4f096892c;hp=065872fbd43182094b94b2526804c33f0d0ef9a4;hpb=a1984b1c8c273ed33c7ce9283039f4027dcae2de;p=jalview.git diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java index 065872f..3dfb510 100644 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -20,29 +20,6 @@ */ package jalview.gui; -import jalview.analysis.AnnotationSorter; -import jalview.api.AlignViewportI; -import jalview.api.AlignmentViewPanel; -import jalview.bin.Cache; -import jalview.bin.Jalview; -import jalview.datamodel.AlignmentI; -import jalview.datamodel.HiddenColumns; -import jalview.datamodel.SearchResultsI; -import jalview.datamodel.SequenceFeature; -import jalview.datamodel.SequenceGroup; -import jalview.datamodel.SequenceI; -import jalview.gui.ImageExporter.ImageWriterI; -import jalview.io.HTMLOutput; -import jalview.jbgui.GAlignmentPanel; -import jalview.math.AlignmentDimension; -import jalview.schemes.ResidueProperties; -import jalview.structure.StructureSelectionManager; -import jalview.util.Comparison; -import jalview.util.ImageMaker; -import jalview.util.MessageManager; -import jalview.viewmodel.ViewportListenerI; -import jalview.viewmodel.ViewportRanges; - import java.awt.BorderLayout; import java.awt.Color; import java.awt.Container; @@ -67,6 +44,32 @@ 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.bin.Console; +import jalview.bin.Jalview; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.HiddenColumns; +import jalview.datamodel.SearchResultsI; +import jalview.datamodel.SequenceFeature; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; +import jalview.gui.ImageExporter.ImageWriterI; +import jalview.io.HTMLOutput; +import jalview.io.exceptions.ImageOutputException; +import jalview.jbgui.GAlignmentPanel; +import jalview.math.AlignmentDimension; +import jalview.schemes.ResidueProperties; +import jalview.structure.StructureSelectionManager; +import jalview.util.Comparison; +import jalview.util.ImageMaker; +import jalview.util.MessageManager; +import jalview.util.imagemaker.BitmapImageSizing; +import jalview.viewmodel.ViewportListenerI; +import jalview.viewmodel.ViewportRanges; + /** * DOCUMENT ME! * @@ -122,7 +125,7 @@ public class AlignmentPanel extends GAlignmentPanel implements */ public AlignmentPanel(AlignFrame af, final AlignViewport av) { -// setBackground(Color.white); // BH 2019 + // setBackground(Color.white); // BH 2019 alignFrame = af; this.av = av; setSeqPanel(new SeqPanel(av, this)); @@ -229,6 +232,10 @@ public class AlignmentPanel extends GAlignmentPanel implements // to prevent drawing old image FontMetrics fm = getFontMetrics(av.getFont()); + // update the flag controlling whether the grid is too small to render the + // font + av.validCharWidth = fm.charWidth('M') <= av.getCharWidth(); + scalePanelHolder.setPreferredSize( new Dimension(10, av.getCharHeight() + fm.getDescent())); idSpaceFillerPanel1.setPreferredSize( @@ -471,8 +478,7 @@ public class AlignmentPanel extends GAlignmentPanel implements /* * Scroll down to make end of search results visible */ - setScrollValues(ranges.getStartRes(), starts + seqIndex - ends - + 1); + setScrollValues(ranges.getStartRes(), starts + seqIndex - ends + 1); } /* * Else results are already visible - no need to scroll @@ -572,7 +578,6 @@ public class AlignmentPanel extends GAlignmentPanel implements Dimension e = idPanel.getSize(); alabels.setSize(new Dimension(e.width, annotationHeight)); - annotationSpaceFillerHolder.setPreferredSize(new Dimension( annotationSpaceFillerHolder.getWidth(), annotationHeight)); annotationScroller.validate(); @@ -806,7 +811,7 @@ public class AlignmentPanel extends GAlignmentPanel implements // could not be validated and it is not clear if it is now being // called. Log warning here in case it is called and unforeseen // problems occur - Cache.warn( + Console.warn( "Unexpected path through code: Wrapped jar file opened with wrap alignment set in preferences"); // scroll to start of panel @@ -1020,8 +1025,8 @@ public class AlignmentPanel extends GAlignmentPanel implements * single graphics context), then reset to (0, scale height) */ alignmentGraphics.translate(alignmentGraphicsOffset, scaleHeight); - getSeqPanel().seqCanvas.drawPanelForPrinting(alignmentGraphics, startRes, - endRes, startSeq, endSeq - 1); + getSeqPanel().seqCanvas.drawPanelForPrinting(alignmentGraphics, + startRes, endRes, startSeq, endSeq - 1); alignmentGraphics.translate(-alignmentGraphicsOffset, 0); if (av.isShowAnnotation() && (endSeq == alignmentHeight)) @@ -1043,6 +1048,7 @@ public class AlignmentPanel extends GAlignmentPanel implements */ alignmentGraphics.translate(alignmentGraphicsOffset, alignmentDrawnHeight); + updateLayout(); getAnnotationPanel().renderer.drawComponent(getAnnotationPanel(), av, alignmentGraphics, -1, startRes, endRes + 1); } @@ -1065,8 +1071,8 @@ public class AlignmentPanel extends GAlignmentPanel implements * * @throws PrinterException */ - public int printWrappedAlignment(int pageWidth, int pageHeight, int pageNumber, - Graphics g) throws PrinterException + public int printWrappedAlignment(int pageWidth, int pageHeight, + int pageNumber, Graphics g) throws PrinterException { getSeqPanel().seqCanvas.calculateWrappedGeometry(getWidth(), getHeight()); @@ -1118,8 +1124,8 @@ public class AlignmentPanel extends GAlignmentPanel implements g.translate(idWidth, 0); - getSeqPanel().seqCanvas.drawWrappedPanelForPrinting(g, pageWidth - idWidth, - totalHeight, 0); + getSeqPanel().seqCanvas.drawWrappedPanelForPrinting(g, + pageWidth - idWidth, totalHeight, 0); if ((pageNumber * pageHeight) < totalHeight) { @@ -1169,14 +1175,23 @@ public class AlignmentPanel extends GAlignmentPanel implements return (w > 0 ? w : calculateIdWidth().width); } + void makeAlignmentImage(ImageMaker.TYPE type, File file, String renderer) throws ImageOutputException + { + makeAlignmentImage(type, file, renderer, + BitmapImageSizing.nullBitmapImageSizing()); + } + /** * Builds an image of the alignment of the specified type (EPS/PNG/SVG) and * writes it to the specified file * * @param type * @param file + * @param textrenderer + * @param bitmapscale */ - void makeAlignmentImage(ImageMaker.TYPE type, File file) + void makeAlignmentImage(ImageMaker.TYPE type, File file, String renderer, + BitmapImageSizing userBis) throws ImageOutputException { final int borderBottomOffset = 5; @@ -1206,7 +1221,8 @@ public class AlignmentPanel extends GAlignmentPanel implements int imageWidth = aDimension.getWidth(); int imageHeight = aDimension.getHeight() + borderBottomOffset; String of = MessageManager.getString("label.alignment"); - exporter.doExport(file, this, imageWidth, imageHeight, of); + exporter.doExport(file, this, imageWidth, imageHeight, of, renderer, + userBis); } /** @@ -1250,7 +1266,7 @@ public class AlignmentPanel extends GAlignmentPanel implements } - public void makePNGImageMap(File imgMapFile, String imageName) + public void makePNGImageMap(File imgMapFile, String imageName) throws ImageOutputException { // /////ONLY WORKS WITH NON WRAPPED ALIGNMENTS // //////////////////////////////////////////// @@ -1284,13 +1300,13 @@ public class AlignmentPanel extends GAlignmentPanel implements String triplet = null; if (av.getAlignment().isNucleotide()) { - triplet = ResidueProperties.nucleotideName.get(seq - .getCharAt(column) + ""); + triplet = ResidueProperties.nucleotideName + .get(seq.getCharAt(column) + ""); } else { - triplet = ResidueProperties.aa2Triplet.get(seq.getCharAt(column) - + ""); + triplet = ResidueProperties.aa2Triplet + .get(seq.getCharAt(column) + ""); } if (triplet == null) @@ -1307,7 +1323,8 @@ public class AlignmentPanel extends GAlignmentPanel implements text.append(" features = seq.findFeatures(column, column); + List features = seq.findFeatures(column, + column); for (SequenceFeature sf : features) { if (sf.isContactFeature()) @@ -1373,7 +1391,7 @@ public class AlignmentPanel extends GAlignmentPanel implements } catch (Exception ex) { - ex.printStackTrace(); + throw new ImageOutputException("couldn't write ImageMap due to unexpected error",ex); } } // /////////END OF IMAGE MAP @@ -1464,9 +1482,9 @@ public class AlignmentPanel extends GAlignmentPanel implements } else { - if (Cache.isDebugEnabled()) + if (Console.isDebugEnabled()) { - Cache.warn("Closing alignment panel which is already closed."); + Console.warn("Closing alignment panel which is already closed."); } } } @@ -1546,11 +1564,12 @@ public class AlignmentPanel extends GAlignmentPanel implements setAlignFrameView(); } } + public void setAlignFrameView() { alignFrame.setDisplayedView(this); } - + @Override public StructureSelectionManager getStructureSelectionManager() { @@ -1740,4 +1759,42 @@ public class AlignmentPanel extends GAlignmentPanel implements return calculationDialog; } + /** + * Constructs and sets the title for the Overview window (if there is one), + * including the align frame's title, and view name (if applicable). Returns + * the title, or null if this panel has no Overview window open. + * + * @param alignFrame + * @return + */ + public String setOverviewTitle(AlignFrame alignFrame) + { + if (this.overviewPanel == null) + { + return null; + } + String overviewTitle = MessageManager + .formatMessage("label.overview_params", new Object[] + { alignFrame.getTitle() }); + String viewName = getViewName(); + if (viewName != null) + { + overviewTitle += (" " + viewName); + } + overviewPanel.setTitle(overviewTitle); + return overviewTitle; + } + + /** + * If this alignment panel has an Overview panel open, closes it + */ + public void closeOverviewPanel() + { + if (overviewPanel != null) + { + overviewPanel.close(); + overviewPanel = null; + } + } + }