X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=552d166133e9c506eca967d148244ecf6a27fc78;hb=ed8a4149077b4debd9d51cca5141287e17b25fad;hp=235c81f068ed8eb17a226e1c780e95bc86b0383e;hpb=134576f5b34894218bdc4c5ce5e27fa18ad973bd;p=jalview.git
diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 235c81f..552d166 100644
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -91,9 +91,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
// this value is set false when selection area being dragged
boolean fastPaint = true;
- int hextent = 0;
+ private int hextent = 0;
- int vextent = 0;
+ private int vextent = 0;
/*
* Flag set while scrolling to follow complementary cDNA/protein scroll. When
@@ -467,7 +467,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
if (res < av.getStartRes() || res >= (av.getStartRes() + cwidth))
{
vscroll.setValue((res / cwidth));
- av.startRes = vscroll.getValue() * cwidth;
+ av.setStartRes(vscroll.getValue() * cwidth);
}
}
@@ -591,7 +591,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
fontChanged();
setAnnotationVisible(av.isShowAnnotation());
boolean wrap = av.getWrapAlignment();
- av.startSeq = 0;
+ av.setStartSeq(0);
scalePanelHolder.setVisible(!wrap);
hscroll.setVisible(!wrap);
idwidthAdjuster.setVisible(!wrap);
@@ -688,7 +688,6 @@ public class AlignmentPanel extends GAlignmentPanel implements
*/
public void setScrollValues(int x, int y)
{
- // System.err.println("Scroll " + this.av.viewName + " to " + x + "," + y);
if (av == null || av.getAlignment() == null)
{
return;
@@ -698,12 +697,10 @@ public class AlignmentPanel extends GAlignmentPanel implements
if (av.hasHiddenColumns())
{
+ // reset the width to exclude hidden columns
width = av.getColumnSelection().findColumnPosition(width);
}
- av.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av
- .getCharWidth())) - 1);
-
hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
vextent = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight();
@@ -737,6 +734,10 @@ public class AlignmentPanel extends GAlignmentPanel implements
x = 0;
}
+ // update endRes after x has (possibly) been adjusted
+ av.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av
+ .getCharWidth())) - 1);
+
/*
* each scroll adjustment triggers adjustmentValueChanged, which resets the
* 'do not scroll complement' flag; ensure it is the same for both
@@ -809,8 +810,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
overviewPanel.setBoxPosition();
}
- int scrollX = av.startRes - oldX;
- int scrollY = av.startSeq - oldY;
+ int scrollX = av.getStartRes() - oldX;
+ int scrollY = av.getStartSeq() - oldY;
if (av.getWrapAlignment() || !fastPaint)
{
@@ -820,13 +821,13 @@ public class AlignmentPanel extends GAlignmentPanel implements
{
// Make sure we're not trying to draw a panel
// larger than the visible window
- if (scrollX > av.endRes - av.startRes)
+ if (scrollX > av.getEndRes() - av.getStartRes())
{
- scrollX = av.endRes - av.startRes;
+ scrollX = av.getEndRes() - av.getStartRes();
}
- else if (scrollX < av.startRes - av.endRes)
+ else if (scrollX < av.getStartRes() - av.getEndRes())
{
- scrollX = av.startRes - av.endRes;
+ scrollX = av.getStartRes() - av.getEndRes();
}
if (scrollX != 0 || scrollY != 0)
@@ -960,7 +961,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
}
else
{
- return printUnwrapped(pwidth, pheight, pi, pg);
+ return printUnwrapped(pwidth, pheight, pi, pg, pg);
}
}
@@ -981,110 +982,103 @@ public class AlignmentPanel extends GAlignmentPanel implements
* @throws PrinterException
* DOCUMENT ME!
*/
- public int printUnwrapped(int pwidth, int pheight, int pi,
- Graphics... pg)
+ /**
+ * Draws the alignment image, including sequence ids, sequences, and
+ * annotation labels and annotations if shown, on either one or two Graphics
+ * context.
+ *
+ * @param pageWidth
+ * @param pageHeight
+ * @param pi
+ * @param idGraphics
+ * the graphics context for sequence ids and annotation labels
+ * @param alignmentGraphics
+ * the graphics context for sequences and annotations (may or may not
+ * be the same context as idGraphics)
+ * @return
+ * @throws PrinterException
+ */
+ public int printUnwrapped(int pageWidth, int pageHeight, int pi,
+ Graphics idGraphics, Graphics alignmentGraphics)
throws PrinterException
{
- boolean isMultiGraphics = pg.length > 1;
- int G0 = 0; // Graphic index of idPanel graphics in multi-graphics mode or
- // entire graphics for non mulit-graphics mode
- int G1 = 0; // Graphic index of alignmentPanel graphics for multi-graphics
- // mode
- if (isMultiGraphics)
- {
- G0 = 0;
- G1 = 1;
- }
+ final int idWidth = getVisibleIdWidth(false);
- int idWidth = getVisibleIdWidth(false);
- FontMetrics fm = getFontMetrics(av.getFont());
- int scaleHeight = av.getCharHeight() + fm.getDescent();
-
- pg[G0].setColor(Color.white);
- pg[G0].fillRect(0, 0, pwidth, pheight);
- pg[G0].setFont(av.getFont());
-
- // //////////////////////////////////
- // / How many sequences and residues can we fit on a printable page?
- int totalRes = (pwidth - idWidth) / av.getCharWidth();
+ /*
+ * 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;
- int totalSeq = (pheight - scaleHeight) / av.getCharHeight() - 1;
+ FontMetrics fm = getFontMetrics(av.getFont());
+ int charHeight = av.getCharHeight();
+ int scaleHeight = charHeight + fm.getDescent();
- int pagesWide = (av.getAlignment().getWidth() / totalRes) + 1;
+ idGraphics.setColor(Color.white);
+ idGraphics.fillRect(0, 0, pageWidth, pageHeight);
+ idGraphics.setFont(av.getFont());
- // ///////////////////////////
- // / Only print these sequences and residues on this page
- int startRes;
+ /*
+ * How many sequences and residues can we fit on a printable page?
+ */
+ int totalRes = (pageWidth - idWidth) / av.getCharWidth();
- // ///////////////////////////
- // / Only print these sequences and residues on this page
- int endRes;
+ int totalSeq = (pageHeight - scaleHeight) / charHeight - 1;
- // ///////////////////////////
- // / Only print these sequences and residues on this page
- int startSeq;
+ int alignmentWidth = av.getAlignment().getWidth();
+ int pagesWide = (alignmentWidth / totalRes) + 1;
- // ///////////////////////////
- // / Only print these sequences and residues on this page
- int endSeq;
- startRes = (pi % pagesWide) * totalRes;
- endRes = (startRes + totalRes) - 1;
+ final int startRes = (pi % pagesWide) * totalRes;
+ int endRes = (startRes + totalRes) - 1;
- if (endRes > (av.getAlignment().getWidth() - 1))
+ if (endRes > (alignmentWidth - 1))
{
- endRes = av.getAlignment().getWidth() - 1;
+ endRes = alignmentWidth - 1;
}
- startSeq = (pi / pagesWide) * totalSeq;
- endSeq = startSeq + totalSeq;
+ final int startSeq = (pi / pagesWide) * totalSeq;
+ int endSeq = startSeq + totalSeq;
- if (endSeq > av.getAlignment().getHeight())
+ int alignmentHeight = av.getAlignment().getHeight();
+ if (endSeq > alignmentHeight)
{
- endSeq = av.getAlignment().getHeight();
+ endSeq = alignmentHeight;
}
- int pagesHigh = ((av.getAlignment().getHeight() / totalSeq) + 1)
- * pheight;
+ int pagesHigh = ((alignmentHeight / totalSeq) + 1)
+ * pageHeight;
if (av.isShowAnnotation())
{
pagesHigh += getAnnotationPanel().adjustPanelHeight() + 3;
}
- pagesHigh /= pheight;
+ pagesHigh /= pageHeight;
if (pi >= (pagesWide * pagesHigh))
{
return Printable.NO_SUCH_PAGE;
}
+ final int alignmentDrawnHeight = (endSeq - startSeq) * charHeight
+ + 3;
- // draw Scale
- if (isMultiGraphics)
- {
- pg[G1].translate(0, 0);
- getScalePanel().drawScale(pg[G1], startRes, endRes,
- pwidth - idWidth, scaleHeight);
- pg[G1].translate(-idWidth, scaleHeight);
- }
- else
- {
- pg[G0].translate(idWidth, 0);
- getScalePanel().drawScale(pg[G0], startRes, endRes, pwidth - idWidth,
- scaleHeight);
- pg[G0].translate(-idWidth, scaleHeight);
- }
+ /*
+ * draw the Scale at horizontal offset, then reset to top left (0, 0)
+ */
+ alignmentGraphics.translate(alignmentGraphicsOffset, 0);
+ getScalePanel().drawScale(alignmentGraphics, startRes, endRes,
+ pageWidth - idWidth, scaleHeight);
+ alignmentGraphics.translate(-alignmentGraphicsOffset, 0);
- // //////////////
- // Draw the ids
+ /*
+ * Draw the sequence ids, offset for scale height,
+ * then reset to top left (0, 0)
+ */
+ idGraphics.translate(0, scaleHeight);
+ idGraphics.setFont(getIdPanel().getIdCanvas().getIdfont());
Color currentColor = null;
Color currentTextColor = null;
- if (isMultiGraphics)
- {
- pg[G0].translate(0, scaleHeight);
- }
- pg[G0].setFont(getIdPanel().getIdCanvas().getIdfont());
-
SequenceI seq;
for (int i = startSeq; i < endSeq; i++)
{
@@ -1092,6 +1086,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
if ((av.getSelectionGroup() != null)
&& av.getSelectionGroup().getSequences(null).contains(seq))
{
+ /*
+ * gray out ids of sequences in selection group (if any)
+ */
currentColor = Color.gray;
currentTextColor = Color.black;
}
@@ -1101,70 +1098,58 @@ public class AlignmentPanel extends GAlignmentPanel implements
currentTextColor = Color.black;
}
- pg[G0].setColor(currentColor);
- pg[G0].fillRect(0, (i - startSeq) * av.getCharHeight(), idWidth,
- av.getCharHeight());
+ idGraphics.setColor(currentColor);
+ idGraphics.fillRect(0, (i - startSeq) * charHeight, idWidth,
+ charHeight);
- pg[G0].setColor(currentTextColor);
+ idGraphics.setColor(currentTextColor);
int xPos = 0;
+ String displayId = seq.getDisplayId(av.getShowJVSuffix());
if (av.isRightAlignIds())
{
- fm = pg[G0].getFontMetrics();
+ fm = idGraphics.getFontMetrics();
xPos = idWidth
- - fm.stringWidth(seq.getDisplayId(av.getShowJVSuffix()))
+ - fm.stringWidth(displayId)
- 4;
}
- pg[G0].drawString(seq.getDisplayId(av.getShowJVSuffix()), xPos,
- (((i - startSeq) * av.getCharHeight()) + av.getCharHeight())
- - (av.getCharHeight() / 5));
+ idGraphics.drawString(displayId, xPos,
+ (((i - startSeq) * charHeight) + charHeight)
+ - (charHeight / 5));
}
+ idGraphics.setFont(av.getFont());
+ idGraphics.translate(0, -scaleHeight);
- pg[G0].setFont(av.getFont());
-
+ /*
+ * draw the sequences, offset for scale height, and id width (if using a
+ * single graphics context), then reset to (0, scale height)
+ */
+ alignmentGraphics.translate(alignmentGraphicsOffset, scaleHeight);
+ getSeqPanel().seqCanvas.drawPanel(alignmentGraphics, startRes, endRes,
+ startSeq, endSeq, 0);
+ alignmentGraphics.translate(-alignmentGraphicsOffset, 0);
- // draw main sequence panel
- pg[G0].translate(idWidth, 0);
- if (isMultiGraphics)
+ if (av.isShowAnnotation() && (endSeq == alignmentHeight))
{
- pg[G1].translate(idWidth, 0);
- getSeqPanel().seqCanvas.drawPanel(pg[G1], startRes, endRes,
- startSeq, endSeq, 0);
- }
- else
- {
- getSeqPanel().seqCanvas.drawPanel(pg[G0], startRes, endRes, startSeq,
- endSeq, 0);
- }
+ /*
+ * draw annotation labels; drawComponent() translates by
+ * getScrollOffset(), so compensate for that first;
+ * then reset to (0, scale height)
+ */
+ int offset = getAlabels().getScrollOffset();
+ idGraphics.translate(0, -offset);
+ idGraphics.translate(0, alignmentDrawnHeight);
+ getAlabels().drawComponent(idGraphics, idWidth);
+ idGraphics.translate(0, -alignmentDrawnHeight);
- if (av.isShowAnnotation() && (endSeq == av.getAlignment().getHeight()))
- {
- // draw annotation label - need to offset for current scroll position
- int offset = -getAlabels().getScrollOffset();
- pg[G0].translate(0, offset);
- pg[G0].translate(-idWidth - 3,
- (endSeq - startSeq) * av.getCharHeight() + 3);
- getAlabels().drawComponent(pg[G0], idWidth);
- pg[G0].translate(idWidth + 3, 0);
- pg[G0].translate(0, -offset);
- if (isMultiGraphics)
- {
- // draw annotation - need to offset for current scroll position
- // pg[G1].translate(0, offset);
- pg[G1].translate(-idWidth - 3,
- (endSeq - startSeq) * av.getCharHeight() + 3);
- pg[G1].translate(idWidth + 3, 0);
- getAnnotationPanel().renderer.drawComponent(getAnnotationPanel(),
- av, pg[G1], -1, startRes, endRes + 1);
- pg[G1].translate(0, -offset);
- }
- else
- {
- getAnnotationPanel().renderer.drawComponent(getAnnotationPanel(),
- av, pg[G0], -1, startRes, endRes + 1);
- pg[G0].translate(0, -offset);
- }
+ /*
+ * draw the annotations starting at
+ * (idOffset, alignmentHeight) from (0, scaleHeight)
+ */
+ alignmentGraphics.translate(alignmentGraphicsOffset, alignmentDrawnHeight);
+ getAnnotationPanel().renderer.drawComponent(getAnnotationPanel(), av,
+ alignmentGraphics, -1, startRes, endRes + 1);
}
return Printable.PAGE_EXISTS;
@@ -1315,8 +1300,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
if (onscreen
|| (idwidth = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH")) == null)
{
- return (getIdPanel().getWidth() > 0 ? getIdPanel().getWidth()
- : calculateIdWidth().width + 4);
+ int w = getIdPanel().getWidth();
+ return (w > 0 ? w : calculateIdWidth().width + 4);
}
return idwidth.intValue() + 4;
}
@@ -1363,22 +1348,23 @@ public class AlignmentPanel extends GAlignmentPanel implements
aDimension.getWidth(), aDimension.getHeight()
+ boarderBottomOffset, file, imageTitle,
alignFrame, pSessionId, headless);
+ Graphics graphics = im.getGraphics();
if (av.getWrapAlignment())
{
- if (im.getGraphics() != null)
+ if (graphics != null)
{
printWrappedAlignment(aDimension.getWidth(),
aDimension.getHeight() + boarderBottomOffset, 0,
- im.getGraphics());
+ graphics);
im.writeImage();
}
}
else
{
- if (im.getGraphics() != null)
+ if (graphics != null)
{
printUnwrapped(aDimension.getWidth(), aDimension.getHeight(),
- 0, im.getGraphics());
+ 0, graphics, graphics);
im.writeImage();
}
}
@@ -1463,7 +1449,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
public void makePNGImageMap(File imgMapFile, String imageName)
{
- // /////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS
+ // /////ONLY WORKS WITH NON WRAPPED ALIGNMENTS
// ////////////////////////////////////////////
int idWidth = getVisibleIdWidth(false);
FontMetrics fm = getFontMetrics(av.getFont());
@@ -1477,7 +1463,6 @@ public class AlignmentPanel extends GAlignmentPanel implements
{
int s, sSize = av.getAlignment().getHeight(), res, alwidth = av
.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("![](\"")
res)
{
- text.append("
" + groups[g].getName() + "");
+ text.append("
").append(groups[g].getName())
+ .append("");
}
}
@@ -1536,12 +1523,13 @@ public class AlignmentPanel extends GAlignmentPanel implements
{
if (text.length() < 1)
{
- text.append("= seq.findPosition(res)))
{
- if (features[f].getType().equals("disulfide bond"))
+ if (features[f].isContactFeature())
{
if (features[f].getBegin() == seq.findPosition(res)
|| features[f].getEnd() == seq
.findPosition(res))
{
- text.append("
disulfide bond "
- + features[f].getBegin() + ":"
- + features[f].getEnd());
+ text.append("
").append(features[f].getType())
+ .append(" ").append(features[f].getBegin())
+ .append(":").append(features[f].getEnd());
}
}
else
@@ -1569,13 +1557,13 @@ public class AlignmentPanel extends GAlignmentPanel implements
&& !features[f].getType().equals(
features[f].getDescription()))
{
- text.append(" " + features[f].getDescription());
+ text.append(" ").append(features[f].getDescription());
}
if (features[f].getValue("status") != null)
{
- text.append(" (" + features[f].getValue("status")
- + ")");
+ text.append(" (").append(features[f].getValue("status"))
+ .append(")");
}
}
}