X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=baac692748cb0b3eef9358216d17056386d66238;hb=refs%2Fheads%2FJAL-2739_2.10.2b1;hp=a732527b7688876772e94e8665d51066b717e1e6;hpb=e54df488cd82761bfb0e9372aeae2acc5a1324d7;p=jalview.git diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java index a732527..baac692 100644 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -70,8 +70,7 @@ import javax.swing.SwingUtilities; * @version $Revision: 1.161 $ */ public class AlignmentPanel extends GAlignmentPanel implements - AdjustmentListener, Printable, AlignmentViewPanel, - ViewportListenerI + AdjustmentListener, Printable, AlignmentViewPanel, ViewportListenerI { public AlignViewport av; @@ -157,8 +156,8 @@ public class AlignmentPanel extends GAlignmentPanel implements // is initialised if (av.getWrapAlignment()) { - int widthInRes = getSeqPanel().seqCanvas - .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth()); + int widthInRes = getSeqPanel().seqCanvas.getWrappedCanvasWidth( + getSeqPanel().seqCanvas.getWidth()); vpRanges.setViewportWidth(widthInRes); } else @@ -167,7 +166,7 @@ public class AlignmentPanel extends GAlignmentPanel implements / av.getCharWidth(); int heightInSeq = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight(); - + vpRanges.setViewportWidth(widthInRes); vpRanges.setViewportHeight(heightInSeq); } @@ -226,11 +225,12 @@ public class AlignmentPanel extends GAlignmentPanel implements // to prevent drawing old image FontMetrics fm = getFontMetrics(av.getFont()); - scalePanelHolder.setPreferredSize(new Dimension(10, av.getCharHeight() - + fm.getDescent())); - idSpaceFillerPanel1.setPreferredSize(new Dimension(10, av - .getCharHeight() + fm.getDescent())); - + scalePanelHolder.setPreferredSize( + new Dimension(10, av.getCharHeight() + fm.getDescent())); + idSpaceFillerPanel1.setPreferredSize( + new Dimension(10, av.getCharHeight() + fm.getDescent())); + idwidthAdjuster.invalidate(); + scalePanelHolder.invalidate(); getIdPanel().getIdCanvas().gg = null; getSeqPanel().seqCanvas.img = null; getAnnotationPanel().adjustPanelHeight(); @@ -289,8 +289,8 @@ public class AlignmentPanel extends GAlignmentPanel implements { Container c = new Container(); - FontMetrics fm = c.getFontMetrics(new Font(av.font.getName(), - Font.ITALIC, av.font.getSize())); + FontMetrics fm = c.getFontMetrics( + new Font(av.font.getName(), Font.ITALIC, av.font.getSize())); AlignmentI al = av.getAlignment(); int i = 0; @@ -331,8 +331,8 @@ public class AlignmentPanel extends GAlignmentPanel implements } } - return new Dimension(maxwidth < 0 ? idWidth : Math.min(maxwidth, - idWidth), 12); + return new Dimension( + maxwidth < 0 ? idWidth : Math.min(maxwidth, idWidth), 12); } /** @@ -477,8 +477,8 @@ public class AlignmentPanel extends GAlignmentPanel implements /* * Scroll down to make end of search results visible */ - setScrollValues(vpRanges.getStartRes(), starts + seqIndex - ends - + 1); + setScrollValues(vpRanges.getStartRes(), + starts + seqIndex - ends + 1); } /* * Else results are already visible - no need to scroll @@ -579,8 +579,8 @@ public class AlignmentPanel extends GAlignmentPanel implements */ if (annotationHeight + alignmentHeight > availableHeight) { - annotationHeight = Math.min(annotationHeight, availableHeight - 2 - * rowHeight); + annotationHeight = Math.min(annotationHeight, + availableHeight - 2 * rowHeight); } } else @@ -590,8 +590,8 @@ public class AlignmentPanel extends GAlignmentPanel implements } hscroll.addNotify(); - annotationScroller.setPreferredSize(new Dimension(annotationScroller - .getWidth(), annotationHeight)); + annotationScroller.setPreferredSize( + new Dimension(annotationScroller.getWidth(), annotationHeight)); Dimension e = idPanel.getSize(); alabels.setSize(new Dimension(e.width, annotationHeight)); @@ -640,9 +640,9 @@ public class AlignmentPanel extends GAlignmentPanel implements } else { - int widthInRes = (canvasWidth / av.getCharWidth()) - 1; - int heightInSeq = (getSeqPanel().seqCanvas.getHeight() / av - .getCharHeight()) - 1; + int widthInRes = (canvasWidth / av.getCharWidth()); + int heightInSeq = (getSeqPanel().seqCanvas.getHeight() + / av.getCharHeight()); vpRanges.setViewportWidth(widthInRes); vpRanges.setViewportHeight(heightInSeq); @@ -654,7 +654,6 @@ public class AlignmentPanel extends GAlignmentPanel implements repaint(); } - /** * Adjust row/column scrollers to show a visible position in the alignment. * @@ -686,7 +685,8 @@ public class AlignmentPanel extends GAlignmentPanel implements if (av.hasHiddenColumns()) { // reset the width to exclude hidden columns - width = av.getAlignment().getHiddenColumns().findColumnPosition(width); + width = av.getAlignment().getHiddenColumns() + .findColumnPosition(width); } hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth(); @@ -809,14 +809,14 @@ public class AlignmentPanel extends GAlignmentPanel implements { return; } - else if (newY > -1) + if (newY > -1) { /* * limit page up/down to one width's worth of positions */ int rowSize = vpRanges.getViewportWidth(); int newX = newY > oldY ? oldX + rowSize : oldX - rowSize; - vpRanges.setViewportStartAndWidth(newX, rowSize); + vpRanges.setViewportStartAndWidth(Math.max(0, newX), rowSize); } } else @@ -828,13 +828,13 @@ public class AlignmentPanel extends GAlignmentPanel implements { @Override public void run() - { + { // When updating scrolling to use ViewportChange events, this code // 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.log - .warn("Unexpected path through code: Wrapped jar file opened with wrap alignment set in preferences"); + Cache.log.warn( + "Unexpected path through code: Wrapped jar file opened with wrap alignment set in preferences"); // scroll to start of panel vpRanges.setStartRes(0); @@ -989,7 +989,8 @@ public class AlignmentPanel extends GAlignmentPanel implements * Get the horizontal offset to where we draw the sequences. * This is idWidth if using a single Graphics context, else zero. */ - final int alignmentGraphicsOffset = idGraphics != alignmentGraphics ? 0 : idWidth; + final int alignmentGraphicsOffset = idGraphics != alignmentGraphics ? 0 + : idWidth; FontMetrics fm = getFontMetrics(av.getFont()); int charHeight = av.getCharHeight(); @@ -1026,8 +1027,7 @@ public class AlignmentPanel extends GAlignmentPanel implements endSeq = alignmentHeight; } - int pagesHigh = ((alignmentHeight / totalSeq) + 1) - * pageHeight; + int pagesHigh = ((alignmentHeight / totalSeq) + 1) * pageHeight; if (av.isShowAnnotation()) { @@ -1040,8 +1040,7 @@ public class AlignmentPanel extends GAlignmentPanel implements { return Printable.NO_SUCH_PAGE; } - final int alignmentDrawnHeight = (endSeq - startSeq) * charHeight - + 3; + final int alignmentDrawnHeight = (endSeq - startSeq) * charHeight + 3; /* * draw the Scale at horizontal offset, then reset to top left (0, 0) @@ -1090,9 +1089,7 @@ public class AlignmentPanel extends GAlignmentPanel implements if (av.isRightAlignIds()) { fm = idGraphics.getFontMetrics(); - xPos = idWidth - - fm.stringWidth(displayId) - - 4; + xPos = idWidth - fm.stringWidth(displayId) - 4; } idGraphics.drawString(displayId, xPos, @@ -1107,8 +1104,8 @@ public class AlignmentPanel extends GAlignmentPanel implements * single graphics context), then reset to (0, scale height) */ alignmentGraphics.translate(alignmentGraphicsOffset, scaleHeight); - getSeqPanel().seqCanvas.drawPanel(alignmentGraphics, startRes, endRes, - startSeq, endSeq, 0); + getSeqPanel().seqCanvas.drawPanelForPrinting(alignmentGraphics, startRes, + endRes, startSeq, endSeq); alignmentGraphics.translate(-alignmentGraphicsOffset, 0); if (av.isShowAnnotation() && (endSeq == alignmentHeight)) @@ -1128,7 +1125,8 @@ public class AlignmentPanel extends GAlignmentPanel implements * draw the annotations starting at * (idOffset, alignmentHeight) from (0, scaleHeight) */ - alignmentGraphics.translate(alignmentGraphicsOffset, alignmentDrawnHeight); + alignmentGraphics.translate(alignmentGraphicsOffset, + alignmentDrawnHeight); getAnnotationPanel().renderer.drawComponent(getAnnotationPanel(), av, alignmentGraphics, -1, startRes, endRes + 1); } @@ -1182,8 +1180,8 @@ public class AlignmentPanel extends GAlignmentPanel implements .findColumnPosition(maxwidth) - 1; } - int resWidth = getSeqPanel().seqCanvas.getWrappedCanvasWidth(pwidth - - idWidth); + int resWidth = getSeqPanel().seqCanvas + .getWrappedCanvasWidth(pwidth - idWidth); int totalHeight = cHeight * (maxwidth / resWidth + 1); @@ -1220,16 +1218,13 @@ public class AlignmentPanel extends GAlignmentPanel implements } if (labels != null) { - pg.translate(-3, - ypos + (av.getAlignment().getHeight() * av.getCharHeight())); + pg.translate(-3, ypos + + (av.getAlignment().getHeight() * av.getCharHeight())); pg.setFont(av.getFont()); labels.drawComponent(pg, idWidth); - pg.translate( - +3, - -ypos - - (av.getAlignment().getHeight() * av - .getCharHeight())); + pg.translate(+3, -ypos + - (av.getAlignment().getHeight() * av.getCharHeight())); } ypos += cHeight; @@ -1237,7 +1232,7 @@ public class AlignmentPanel extends GAlignmentPanel implements pg.translate(idWidth, 0); - getSeqPanel().seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, + getSeqPanel().seqCanvas.drawWrappedPanelForPrinting(pg, pwidth - idWidth, totalHeight, 0); if ((pi * pheight) < totalHeight) @@ -1279,8 +1274,8 @@ public class AlignmentPanel extends GAlignmentPanel implements return calculateIdWidth(-1).width + 4; } Integer idwidth = null; - if (onscreen - || (idwidth = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH")) == null) + if (onscreen || (idwidth = Cache + .getIntegerProperty("FIGURE_FIXEDIDWIDTH")) == null) { int w = getIdPanel().getWidth(); return (w > 0 ? w : calculateIdWidth().width + 4); @@ -1292,15 +1287,15 @@ public class AlignmentPanel extends GAlignmentPanel implements { int boarderBottomOffset = 5; long pSessionId = System.currentTimeMillis(); - headless = (System.getProperty("java.awt.headless") != null && System - .getProperty("java.awt.headless").equals("true")); + headless = (System.getProperty("java.awt.headless") != null + && System.getProperty("java.awt.headless").equals("true")); if (alignFrame != null && !headless) { if (file != null) { - alignFrame.setProgressBar(MessageManager.formatMessage( - "status.saving_file", new Object[] { type.getLabel() }), - pSessionId); + alignFrame.setProgressBar(MessageManager + .formatMessage("status.saving_file", new Object[] + { type.getLabel() }), pSessionId); } } try @@ -1327,9 +1322,9 @@ public class AlignmentPanel extends GAlignmentPanel implements } im = new jalview.util.ImageMaker(this, type, imageAction, - aDimension.getWidth(), aDimension.getHeight() - + boarderBottomOffset, file, imageTitle, - alignFrame, pSessionId, headless); + aDimension.getWidth(), + aDimension.getHeight() + boarderBottomOffset, file, + imageTitle, alignFrame, pSessionId, headless); Graphics graphics = im.getGraphics(); if (av.getWrapAlignment()) { @@ -1345,8 +1340,8 @@ public class AlignmentPanel extends GAlignmentPanel implements { if (graphics != null) { - printUnwrapped(aDimension.getWidth(), aDimension.getHeight(), - 0, graphics, graphics); + printUnwrapped(aDimension.getWidth(), aDimension.getHeight(), 0, + graphics, graphics); im.writeImage(); } } @@ -1391,9 +1386,8 @@ public class AlignmentPanel extends GAlignmentPanel implements // this duplicates the calculation in getWrappedHeight but adjusts for // offscreen idWith width = alignFrame.getWidth() - vscroll.getPreferredSize().width - - alignFrame.getInsets().left - - alignFrame.getInsets().right - getVisibleIdWidth() - + getVisibleIdWidth(false); + - alignFrame.getInsets().left - alignFrame.getInsets().right + - getVisibleIdWidth() + getVisibleIdWidth(false); } else { @@ -1444,8 +1438,9 @@ public class AlignmentPanel extends GAlignmentPanel implements { try { - int s, sSize = av.getAlignment().getHeight(), res, alwidth = av - .getAlignment().getWidth(), g, gSize, f, fSize, sy; + int s, sSize = av.getAlignment().getHeight(), res, + alwidth = av.getAlignment().getWidth(), g, gSize, f, fSize, + sy; PrintWriter out = new PrintWriter(new FileWriter(imgMapFile)); out.println(jalview.io.HTMLOutput.getImageMapHTML()); out.println(""); text.append(features[f].getType()); - if (features[f].getDescription() != null - && !features[f].getType().equals( - features[f].getDescription())) + if (features[f].getDescription() != null && !features[f] + .getType().equals(features[f].getDescription())) { text.append(" ").append(features[f].getDescription()); } if (features[f].getValue("status") != null) { - text.append(" (").append(features[f].getValue("status")) + text.append(" (") + .append(features[f].getValue("status")) .append(")"); } } @@ -1903,7 +1898,7 @@ public class AlignmentPanel extends GAlignmentPanel implements @Override /** - * Property change event fired when a change is made to the viewport ranges + * Property change event fired when a change is made to the viewport ranges * object associated with this alignment panel's viewport */ public void propertyChange(PropertyChangeEvent evt)