X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=59a6cb1072b4128b4445c47840a6cbb148c35c67;hb=d3bf4ae12b72df02dee34c95da750ab38a3816b9;hp=8ad094f4bf88b2c15d1df4911ebd65712c1f9dd1;hpb=2677eb3d3744f321876e25eeaa70dfa8fde70184;p=jalview.git diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java index 8ad094f..59a6cb1 100755 --- a/src/jalview/gui/SeqCanvas.java +++ b/src/jalview/gui/SeqCanvas.java @@ -25,85 +25,95 @@ import jalview.datamodel.HiddenColumns; import jalview.datamodel.SearchResultsI; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; +import jalview.datamodel.VisibleContigsIterator; import jalview.renderer.ScaleRenderer; import jalview.renderer.ScaleRenderer.ScaleMark; import jalview.util.Comparison; import jalview.viewmodel.ViewportListenerI; import jalview.viewmodel.ViewportRanges; -import java.awt.AlphaComposite; // ok import java.awt.BasicStroke; import java.awt.BorderLayout; import java.awt.Color; import java.awt.FontMetrics; import java.awt.Graphics; import java.awt.Graphics2D; +import java.awt.Rectangle; import java.awt.RenderingHints; -import java.awt.Shape; import java.awt.image.BufferedImage; import java.beans.PropertyChangeEvent; +import java.util.Iterator; import java.util.List; -import javax.swing.JComponent; +import javax.swing.JPanel; /** - * DOCUMENT ME! + * The Swing component on which the alignment sequences, and annotations (if + * shown), are drawn. This includes scales above, left and right (if shown) in + * Wrapped mode, but not the scale above in Unwrapped mode. * - * @author $author$ - * @version $Revision$ */ -public class SeqCanvas extends JComponent implements ViewportListenerI +@SuppressWarnings("serial") +public class SeqCanvas extends JPanel implements ViewportListenerI { - private static String ZEROS = "0000000000"; + /** + * vertical gap in pixels between sequences and annotations when in wrapped + * mode + */ + static final int SEQS_ANNOTATION_GAP = 3; - final FeatureRenderer fr; + private static final String ZEROS = "0000000000"; - final SequenceRenderer seqRdr; //ok + final FeatureRenderer fr; BufferedImage img; - Graphics2D gg; - - int imgWidth; - - int imgHeight; - AlignViewport av; - boolean fastPaint = false; - - boolean fastpainting = false; - int cursorX = 0; int cursorY = 0; + private final SequenceRenderer seqRdr; + + private boolean fastPaint = false; + + private boolean fastpainting = false; + private AnnotationPanel annotations; /* * measurements for drawing a wrapped alignment */ - int labelWidthWest; // label left width in pixels if shown - private int labelWidthEast; // label right width in pixels if shown - private int wrappedSpaceAboveAlignment; // gap between widths + private int labelWidthWest; // label left width in pixels if shown + + int wrappedSpaceAboveAlignment; // gap between widths - private int wrappedRepeatHeightPx; // height in pixels of wrapped width + int wrappedRepeatHeightPx; // height in pixels of wrapped width private int wrappedVisibleWidths; // number of wrapped widths displayed + private int availWidth; + + private int availHeight; + + private boolean allowFastPaint; + + // Don't do this! Graphics handles are supposed to be transient + // private Graphics2D gg; + /** * Creates a new SeqCanvas object. * - * @param av - * DOCUMENT ME! + * @param ap */ public SeqCanvas(AlignmentPanel ap) { this.av = ap.av; fr = new FeatureRenderer(ap); - seqRdr = new SequenceRenderer(av); //ok + seqRdr = new SequenceRenderer(av); setLayout(new BorderLayout()); PaintRefresher.Register(this, av.getSequenceSetId()); setBackground(Color.white); @@ -113,7 +123,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI public SequenceRenderer getSequenceRenderer() { - return seqRdr; //ok + return seqRdr; } public FeatureRenderer getFeatureRenderer() @@ -190,19 +200,21 @@ public class SeqCanvas extends JComponent implements ViewportListenerI * @param left * if true, scale is left of residues, if false, scale is right */ - void drawVerticalScale(Graphics g, int startx, int endx, int ypos, - boolean left) + void drawVerticalScale(Graphics g, final int startx, final int endx, + final int ypos, final boolean left) { int charHeight = av.getCharHeight(); int charWidth = av.getCharWidth(); - ypos += charHeight; + int yPos = ypos + charHeight; + int startX = startx; + int endX = endx; if (av.hasHiddenColumns()) { HiddenColumns hiddenColumns = av.getAlignment().getHiddenColumns(); - startx = hiddenColumns.adjustForHiddenColumns(startx); - endx = hiddenColumns.adjustForHiddenColumns(endx); + startX = hiddenColumns.visibleToAbsoluteColumn(startx); + endX = hiddenColumns.visibleToAbsoluteColumn(endx); } FontMetrics fm = getFontMetrics(av.getFont()); @@ -214,9 +226,9 @@ public class SeqCanvas extends JComponent implements ViewportListenerI * find sequence position of first non-gapped position - * to the right if scale left, to the left if scale right */ - int index = left ? startx : endx; + int index = left ? startX : endX; int value = -1; - while (index >= startx && index <= endx) + while (index >= startX && index <= endX) { if (!Comparison.isGap(seq.getCharAt(index))) { @@ -237,29 +249,29 @@ public class SeqCanvas extends JComponent implements ViewportListenerI * white fill the space for the scale */ g.setColor(Color.white); - int y = (ypos + (i * charHeight)) - (charHeight / 5); + int y = (yPos + (i * charHeight)) - (charHeight / 5); // fillRect origin is top left of rectangle g.fillRect(0, y - charHeight, left ? labelWidthWest : labelWidthEast, charHeight + 1); if (value != -1) { - /* - * draw scale value, right justified, with half a character width - * separation from the sequence data + * draw scale value, right justified within its width less half a + * character width padding on the right */ + int labelSpace = left ? labelWidthWest : labelWidthEast; + labelSpace -= charWidth / 2; // leave space to the right String valueAsString = String.valueOf(value); - int justify = fm.stringWidth(valueAsString) + charWidth; - int xpos = left ? labelWidthWest - justify + charWidth / 2 - : labelWidthEast - justify + charWidth / 2; + int labelLength = fm.stringWidth(valueAsString); + int xOffset = labelSpace - labelLength; g.setColor(Color.black); - g.drawString(valueAsString, xpos, y); + g.drawString(valueAsString, xOffset, y); } } + } - //ok /** * Does a fast paint of an alignment in response to a scroll. Most of the * visible region is simply copied and shifted, and then any newly visible @@ -271,6 +283,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI *
- * Currently fastPaint is not implemented for wrapped alignments. If a wrapped - * alignment had to be scrolled to show the highlighted region, then it should - * be fully redrawn, otherwise a fast paint can be performed. This argument - * could be removed if fast paint of scrolled wrapped alignment is coded in - * future (JAL-2609). + * Optionally, set the 'fastPaint' flag for a faster redraw if only the + * highlighted regions are modified. This speeds up highlighting across linked + * alignments. + *
+ * Currently fastPaint is not implemented for scrolled wrapped alignments. If + * a wrapped alignment had to be scrolled to show the highlighted region, then + * it should be fully redrawn, otherwise a fast paint can be performed. This + * argument could be removed if fast paint of scrolled wrapped alignment is + * coded in future (JAL-2609). * * @param results - * @param noFastPaint + * @param doFastPaint + * if true, sets a flag so the next repaint only redraws the modified + * image * @return */ public boolean highlightSearchResults(SearchResultsI results, - boolean noFastPaint) + boolean doFastPaint) { if (fastpainting) { @@ -1525,7 +1561,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI boolean wrapped = av.getWrapAlignment(); try { - fastPaint = !noFastPaint; + fastPaint = doFastPaint; fastpainting = fastPaint; /* @@ -1582,7 +1618,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI */ protected boolean drawMappedPositions(SearchResultsI results) { - if (results == null) + if ((results == null) || (img == null)) // JAL-2784 check gg is not null { return false; } @@ -1604,9 +1640,9 @@ public class SeqCanvas extends JComponent implements ViewportListenerI if (av.hasHiddenColumns()) { firstVisibleColumn = alignment.getHiddenColumns() - .adjustForHiddenColumns(firstVisibleColumn); + .visibleToAbsoluteColumn(firstVisibleColumn); lastVisibleColumn = alignment.getHiddenColumns() - .adjustForHiddenColumns(lastVisibleColumn); + .visibleToAbsoluteColumn(lastVisibleColumn); } for (int seqNo = ranges.getStartSeq(); seqNo <= ranges @@ -1649,14 +1685,17 @@ public class SeqCanvas extends JComponent implements ViewportListenerI if (av.hasHiddenColumns()) { firstCol = alignment.getHiddenColumns() - .findColumnPosition(firstCol); - lastCol = alignment.getHiddenColumns().findColumnPosition(lastCol); + .absoluteToVisibleColumn(firstCol); + lastCol = alignment.getHiddenColumns() + .absoluteToVisibleColumn(lastCol); } int transX = (firstCol - ranges.getStartRes()) * av.getCharWidth(); int transY = (firstSeq - ranges.getStartSeq()) * av.getCharHeight(); + Graphics gg = img.getGraphics(); gg.translate(transX, transY); drawPanel(gg, firstCol, lastCol, firstSeq, lastSeq, 0); gg.translate(-transX, -transY); + gg.dispose(); } return matchFound; @@ -1667,52 +1706,157 @@ public class SeqCanvas extends JComponent implements ViewportListenerI { String eventName = evt.getPropertyName(); - if (eventName.equals(SequenceGroup.SEQ_GROUP_CHANGED)) + // BH 2019.07.27 removes dead code introduced in aad3650 and simplifies + // logic, emphasizing no check for ENDRES or ENDSEQ + + // Both scrolling and resizing change viewport ranges: scrolling changes + // both start and end points, but resize only changes end values. + // Here we only want to fastpaint on a scroll, with resize using a normal + // paint, so scroll events are identified as changes to the horizontal or + // vertical start value. + + // Make sure we're not trying to draw a panel + // larger than the visible window + int scrollX = 0; + int scrollY = 0; + switch (eventName) { + case SequenceGroup.SEQ_GROUP_CHANGED: fastPaint = true; repaint(); - } - else if (eventName.equals(ViewportRanges.STARTRES)) - { - int scrollX = 0; - if (eventName.equals(ViewportRanges.STARTRES)) + return; + case ViewportRanges.MOVE_VIEWPORT: + fastPaint = false; + repaint(); + return; + case ViewportRanges.STARTSEQ: + // meaning STARTOREND + // typically scroll, but possibly just the end changed + fastPaint(0, (int) evt.getNewValue() - (int) evt.getOldValue()); + return; + case ViewportRanges.STARTRES: + // meaning STARTOREND + scrollX = (int) evt.getNewValue() - (int) evt.getOldValue(); + break; + case ViewportRanges.STARTRESANDSEQ: + scrollX = ((int[]) evt.getNewValue())[0] + - ((int[]) evt.getOldValue())[0]; + scrollY = ((int[]) evt.getNewValue())[1] + - ((int[]) evt.getOldValue())[1]; + if (scrollX != 0 && scrollY != 0) { - // Make sure we're not trying to draw a panel - // larger than the visible window - ViewportRanges vpRanges = av.getRanges(); - scrollX = (int) evt.getNewValue() - (int) evt.getOldValue(); - int range = vpRanges.getEndRes() - vpRanges.getStartRes(); - if (scrollX > range) - { - scrollX = range; - } - else if (scrollX < -range) - { - scrollX = -range; - } + // all sorts of problems in JavaScript if this is commented out. + repaint(); + return; - // Both scrolling and resizing change viewport ranges: scrolling changes - // both start and end points, but resize only changes end values. - // Here we only want to fastpaint on a scroll, with resize using a normal - // paint, so scroll events are identified as changes to the horizontal or - // vertical start value. - - // scroll - startres and endres both change - if (av.getWrapAlignment()) - { - fastPaintWrapped(scrollX); - } - else - { - fastPaint(scrollX, 0); - } - } - else if (eventName.equals(ViewportRanges.STARTSEQ)) - { - // scroll - fastPaint(0, (int) evt.getNewValue() - (int) evt.getOldValue()); } + break; + default: + return; + } + + ViewportRanges vpRanges = av.getRanges(); + int range = vpRanges.getEndRes() - vpRanges.getStartRes() + 1; + scrollX = Math.max(Math.min(scrollX, range), -range); + // only STARTRES or STARTRESANDSEQ: + if (av.getWrapAlignment()) + { + fastPaintWrapped(scrollX); } + else + { + fastPaint(scrollX, scrollY); + } + + // BH 2019.07.27 was: + // if (eventName.equals(SequenceGroup.SEQ_GROUP_CHANGED)) + // { + // fastPaint = true; + // repaint(); + // return; + // } + // else if (eventName.equals(ViewportRanges.MOVE_VIEWPORT)) + // { + // fastPaint = false; + // // System.err.println("!!!! fastPaint false from MOVE_VIEWPORT"); + // repaint(); + // return; + // } + // + // if (eventName.equals(ViewportRanges.STARTRES) + // || eventName.equals(ViewportRanges.STARTRESANDSEQ)) + // { + // // Make sure we're not trying to draw a panel + // // larger than the visible window + // if (eventName.equals(ViewportRanges.STARTRES)) + // { + // scrollX = (int) evt.getNewValue() - (int) evt.getOldValue(); + // } + // else + // { + // scrollX = ((int[]) evt.getNewValue())[0] + // - ((int[]) evt.getOldValue())[0]; + // } + // ViewportRanges vpRanges = av.getRanges(); + // + // int range = vpRanges.getEndRes() - vpRanges.getStartRes() + 1; + // if (scrollX > range) + // { + // scrollX = range; + // } + // else if (scrollX < -range) + // { + // scrollX = -range; + // } + // } + // Both scrolling and resizing change viewport ranges: scrolling changes + // both start and end points, but resize only changes end values. + // Here we only want to fastpaint on a scroll, with resize using a normal + // paint, so scroll events are identified as changes to the horizontal or + // vertical start value. + // BH 2019.07.27 was: + // if (eventName.equals(ViewportRanges.STARTRES)) + // { + // if (av.getWrapAlignment()) + // { + // fastPaintWrapped(scrollX); + // } + // else + // { + // fastPaint(scrollX, 0); + // } + // } + // else if (eventName.equals(ViewportRanges.STARTSEQ)) + // { + // // scroll + // fastPaint(0, (int) evt.getNewValue() - (int) evt.getOldValue()); + // } + // else if (eventName.equals(ViewportRanges.STARTRESANDSEQ)) + // { + // if (av.getWrapAlignment()) + // { + // fastPaintWrapped(scrollX); + // } + // else + // { + // fastPaint(scrollX, 0); + // } + // } + // + // BH oops! + // + // else if (eventName.equals(ViewportRanges.STARTSEQ)) + // { + // // scroll + // fastPaint(0, (int) evt.getNewValue() - (int) evt.getOldValue()); + // } + // else if (eventName.equals(ViewportRanges.STARTRESANDSEQ)) + // { + // if (av.getWrapAlignment()) + // { + // fastPaintWrapped(scrollX); + // } + // } } /** @@ -1728,10 +1872,10 @@ public class SeqCanvas extends JComponent implements ViewportListenerI { ViewportRanges ranges = av.getRanges(); - if (Math.abs(scrollX) > ranges.getViewportWidth()) + if (Math.abs(scrollX) >= ranges.getViewportWidth()) { /* - * shift of more than one view width is + * shift of one view width or more is * overcomplicated to handle in this method */ fastPaint = false; @@ -1739,7 +1883,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI return; } - if (fastpainting || gg == null) + if (fastpainting || img == null) { return; } @@ -1749,7 +1893,10 @@ public class SeqCanvas extends JComponent implements ViewportListenerI try { - calculateWrappedGeometry(getWidth(), getHeight()); + + Graphics gg = img.getGraphics(); + + calculateWrappedGeometry(); /* * relocate the regions of the alignment that are still visible @@ -1764,8 +1911,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI if (scrollX < 0) { int startRes = ranges.getStartRes(); - drawWrappedWidth(gg, wrappedSpaceAboveAlignment, startRes, startRes - - scrollX - 1, getHeight()); + drawWrappedWidth(gg, wrappedSpaceAboveAlignment, startRes, + startRes - scrollX - 1, getHeight()); } else { @@ -1777,6 +1924,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI */ drawWrappedDecorators(gg, ranges.getStartRes()); + gg.dispose(); + repaint(); } finally { @@ -1800,6 +1949,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI return; } + Graphics gg = img.getGraphics(); + ViewportRanges ranges = av.getRanges(); int viewportWidth = ranges.getViewportWidth(); int charWidth = av.getCharWidth(); @@ -1810,7 +1961,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI */ int visibleWidths = wrappedVisibleWidths; int canvasHeight = getHeight(); - boolean lastWidthPartHeight = (wrappedVisibleWidths * wrappedRepeatHeightPx) > canvasHeight; + boolean lastWidthPartHeight = (wrappedVisibleWidths + * wrappedRepeatHeightPx) > canvasHeight; if (lastWidthPartHeight) { @@ -1826,13 +1978,15 @@ public class SeqCanvas extends JComponent implements ViewportListenerI /* * white fill first to erase annotations */ + gg.translate(xOffset, 0); gg.setColor(Color.white); - gg.fillRect(labelWidthWest, ypos, - (endRes - startRes + 1) * charWidth, wrappedRepeatHeightPx); + gg.fillRect(labelWidthWest, ypos, (endRes - startRes + 1) * charWidth, + wrappedRepeatHeightPx); gg.translate(-xOffset, 0); drawWrappedWidth(gg, ypos, startRes, endRes, canvasHeight); + } /* @@ -1876,6 +2030,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI gg.setColor(Color.white); gg.fillRect(0, canvasHeight - heightBelow, getWidth(), heightBelow); } + gg.dispose(); } /** @@ -1892,6 +2047,9 @@ public class SeqCanvas extends JComponent implements ViewportListenerI { return; } + + Graphics gg = img.getGraphics(); + int charWidth = av.getCharWidth(); int canvasHeight = getHeight(); @@ -1922,10 +2080,17 @@ public class SeqCanvas extends JComponent implements ViewportListenerI while (y >= 0) { + /* + * shift 'widthToCopy' residues by 'positions' places to the right + */ gg.copyArea(copyFromLeftStart, y, widthToCopy, heightToCopy, positions * charWidth, 0); if (y > 0) { + /* + * copy 'positions' residue from the row above (right hand end) + * to this row's left hand end + */ gg.copyArea(copyFromRightStart, y - wrappedRepeatHeightPx, positions * charWidth, heightToCopy, -widthToCopy, wrappedRepeatHeightPx); @@ -1954,18 +2119,17 @@ public class SeqCanvas extends JComponent implements ViewportListenerI if (y + wrappedRepeatHeightPx < canvasHeight - wrappedRepeatHeightPx && (xpos + viewportWidth <= xMax)) { - gg.copyArea(labelWidthWest, y + wrappedRepeatHeightPx, -positions - * charWidth, heightToCopy, widthToCopy, + gg.copyArea(labelWidthWest, y + wrappedRepeatHeightPx, + -positions * charWidth, heightToCopy, widthToCopy, -wrappedRepeatHeightPx); } - y += wrappedRepeatHeightPx; xpos += viewportWidth; } } + gg.dispose(); } - /** * Redraws any positions in the search results in the visible region of a * wrapped alignment. Any highlights are drawn depending on the search results @@ -1978,7 +2142,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI */ protected boolean drawMappedPositionsWrapped(SearchResultsI results) { - if (results == null) + if ((results == null) || (img == null)) // JAL-2784 check gg is not null { return false; } @@ -1986,7 +2150,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI boolean matchFound = false; - calculateWrappedGeometry(getWidth(), getHeight()); + calculateWrappedGeometry(); int wrappedWidth = av.getWrappedWidth(); int wrappedHeight = wrappedRepeatHeightPx; @@ -1999,20 +2163,22 @@ public class SeqCanvas extends JComponent implements ViewportListenerI } int firstVisibleColumn = ranges.getStartRes(); - int lastVisibleColumn = ranges.getStartRes() + repeats - * ranges.getViewportWidth() - 1; + int lastVisibleColumn = ranges.getStartRes() + + repeats * ranges.getViewportWidth() - 1; AlignmentI alignment = av.getAlignment(); if (av.hasHiddenColumns()) { firstVisibleColumn = alignment.getHiddenColumns() - .adjustForHiddenColumns(firstVisibleColumn); + .visibleToAbsoluteColumn(firstVisibleColumn); lastVisibleColumn = alignment.getHiddenColumns() - .adjustForHiddenColumns(lastVisibleColumn); + .visibleToAbsoluteColumn(lastVisibleColumn); } int gapHeight = charHeight * (av.getScaleAboveWrapped() ? 2 : 1); + Graphics gg = img.getGraphics(); + for (int seqNo = ranges.getStartSeq(); seqNo <= ranges .getEndSeq(); seqNo++) { @@ -2047,15 +2213,15 @@ public class SeqCanvas extends JComponent implements ViewportListenerI if (av.hasHiddenColumns()) { displayColumn = alignment.getHiddenColumns() - .findColumnPosition(displayColumn); + .absoluteToVisibleColumn(displayColumn); } /* * transX: offset from left edge of canvas to residue position */ int transX = labelWidthWest - + ((displayColumn - ranges.getStartRes()) % wrappedWidth) - * av.getCharWidth(); + + ((displayColumn - ranges.getStartRes()) + % wrappedWidth) * av.getCharWidth(); /* * transY: offset from top edge of canvas to residue position @@ -2082,7 +2248,29 @@ public class SeqCanvas extends JComponent implements ViewportListenerI } } } - + + gg.dispose(); + return matchFound; } + + /** + * Answers the width in pixels of the left scale labels (0 if not shown) + * + * @return + */ + int getLabelWidthWest() + { + return labelWidthWest; + } + + /** + * Clears the flag that allows a 'fast paint' on the next repaint, so + * requiring a full repaint + */ + public void setNoFastPaint() + { + allowFastPaint = false; + } + }