public Dimension calculateIdWidth()
{
// calculate sensible default width when no preference is available
-
+
int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300);
int maxwidth = Math.max(20,
Math.min(afwidth - 200, (int) 2 * afwidth / 3));
return calculateIdWidth(maxwidth);
}
+
/**
* Calculate the width of the alignment labels based on the displayed names
* and any bounds on label width set in preferences.
- * @param maxwidth -1 or maximum width allowed for IdWidth
+ *
+ * @param maxwidth
+ * -1 or maximum width allowed for IdWidth
* @return Dimension giving the maximum width of the alignment label panel
* that should be used.
*/
}
}
- return new Dimension(maxwidth<0 ? idWidth : Math.min(maxwidth, idWidth), 12);
+ return new Dimension(maxwidth < 0 ? idWidth : Math.min(maxwidth,
+ idWidth), 12);
}
/**
return false;
}
SequenceI seq = av.getAlignment().getSequenceAt(seqIndex);
-
- int[] r=results.getResults(seq, 0, av.getAlignment().getWidth());
+
+ int[] r = results.getResults(seq, 0, av.getAlignment().getWidth());
if (r == null)
{
return false;
{
start = av.getColumnSelection().findColumnPosition(start);
end = av.getColumnSelection().findColumnPosition(end);
- if (start==end)
+ if (start == end)
{
if (!av.getColumnSelection().isVisible(r[0]))
{
/**
*
- * @param b Hide or show annotation panel
- *
+ * @param b
+ * Hide or show annotation panel
+ *
*/
public void setAnnotationVisible(boolean b)
{
}
/**
- * automatically adjust annotation panel height for new annotation
- * whilst ensuring the alignment is still visible.
+ * automatically adjust annotation panel height for new annotation whilst
+ * ensuring the alignment is still visible.
*/
public void adjustAnnotationHeight()
{
addNotify();
paintAlignment(true);
}
+
/**
* calculate the annotation dimensions and refresh slider values accordingly.
- * need to do repaints/notifys afterwards.
+ * need to do repaints/notifys afterwards.
*/
- protected void validateAnnotationDimensions(boolean adjustPanelHeight) {
+ protected void validateAnnotationDimensions(boolean adjustPanelHeight)
+ {
int height = annotationPanel.adjustPanelHeight();
-
+
if (hscroll.isVisible())
{
height += hscroll.getPreferredSize().height;
if (!adjustPanelHeight)
{
// maintain same window layout whilst updating sliders
- height=annotationScroller.getSize().height;
+ height = annotationScroller.getSize().height;
}
hscroll.addNotify();
-
+
annotationScroller.setPreferredSize(new Dimension(annotationScroller
.getWidth(), height));
/**
* Adjust row/column scrollers to show a visible position in the alignment.
*
- * @param x visible column to scroll to
- * DOCUMENT ME!
- * @param y visible row to scroll to
- *
+ * @param x
+ * visible column to scroll to DOCUMENT ME!
+ * @param y
+ * visible row to scroll to
+ *
*/
public void setScrollValues(int x, int y)
{
endSeq = av.getAlignment().getHeight();
}
- int pagesHigh = ((av.getAlignment().getHeight() / totalSeq) + 1) * pheight;
+ int pagesHigh = ((av.getAlignment().getHeight() / totalSeq) + 1)
+ * pheight;
if (av.showAnnotation)
{
if (av.showAnnotation && (endSeq == av.getAlignment().getHeight()))
{
// draw annotation - need to offset for current scroll position
- int offset=-alabels.scrollOffset;
+ int offset = -alabels.scrollOffset;
pg.translate(0, offset);
pg.translate(-idWidth - 3, (endSeq - startSeq) * av.charHeight + 3);
alabels.drawComponent((Graphics2D) pg, idWidth);
pg.translate(idWidth + 3, 0);
- annotationPanel.renderer.drawComponent(annotationPanel, av, (Graphics2D) pg, -1, startRes, endRes + 1);
+ annotationPanel.renderer.drawComponent(annotationPanel, av,
+ (Graphics2D) pg, -1, startRes, endRes + 1);
pg.translate(0, -offset);
}
return Printable.NO_SUCH_PAGE;
}
}
+
/**
- * get current sequence ID panel width, or nominal value if panel were to be displayed using default settings
+ * get current sequence ID panel width, or nominal value if panel were to be
+ * displayed using default settings
+ *
* @return
*/
int getVisibleIdWidth()
}
/**
- * get current sequence ID panel width, or nominal value if panel were to be displayed using default settings
- * @param onscreen indicate if the Id width for onscreen or offscreen display should be returned
+ * get current sequence ID panel width, or nominal value if panel were to be
+ * displayed using default settings
+ *
+ * @param onscreen
+ * indicate if the Id width for onscreen or offscreen display should
+ * be returned
* @return
*/
int getVisibleIdWidth(boolean onscreen)
// see if rendering offscreen - check preferences and calc width accordingly
if (!onscreen && Cache.getDefault("FIGURE_AUTOIDWIDTH", false))
{
- return calculateIdWidth(-1).width+4;
+ return calculateIdWidth(-1).width + 4;
}
- Integer idwidth=null;
- if (onscreen || (idwidth=Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH"))==null) {
+ Integer idwidth = null;
+ if (onscreen
+ || (idwidth = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH")) == null)
+ {
return (idPanel.getWidth() > 0 ? idPanel.getWidth()
- : calculateIdWidth().width + 4);
+ : calculateIdWidth().width + 4);
}
- return idwidth.intValue()+4;
+ return idwidth.intValue() + 4;
}
void makeAlignmentImage(int type, File file)
{
- long progress=System.currentTimeMillis();
- if (alignFrame!=null) {
- alignFrame.setProgressBar("Saving "+(type == jalview.util.ImageMaker.PNG ? "PNG image":"EPS file") , progress);
- }
- try {
- int maxwidth = av.getAlignment().getWidth();
- if (av.hasHiddenColumns())
+ long progress = System.currentTimeMillis();
+ if (alignFrame != null)
{
- maxwidth = av.getColumnSelection().findColumnPosition(maxwidth);
+ alignFrame.setProgressBar("Saving "
+ + (type == jalview.util.ImageMaker.PNG ? "PNG image"
+ : "EPS file"), progress);
}
-
- int height = ((av.getAlignment().getHeight() + 1) * av.charHeight)
- + scalePanel.getHeight();
- int width = getVisibleIdWidth(false) + (maxwidth * av.charWidth);
-
- if (av.getWrapAlignment())
+ try
{
- height = getWrappedHeight();
- if (System.getProperty("java.awt.headless") != null
- && System.getProperty("java.awt.headless").equals("true"))
- {
- // need to obtain default alignment width and then add in any additional allowance for id margin
- // 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);
- }
- else
+ int maxwidth = av.getAlignment().getWidth();
+ if (av.hasHiddenColumns())
{
- width = seqPanel.getWidth() + getVisibleIdWidth(false);
+ maxwidth = av.getColumnSelection().findColumnPosition(maxwidth);
}
- }
- else if (av.getShowAnnotation())
- {
- height += annotationPanel.adjustPanelHeight() + 3;
- }
-
- try
- {
+ int height = ((av.getAlignment().getHeight() + 1) * av.charHeight)
+ + scalePanel.getHeight();
+ int width = getVisibleIdWidth(false) + (maxwidth * av.charWidth);
- jalview.util.ImageMaker im;
- final String imageAction,imageTitle;
- if (type == jalview.util.ImageMaker.PNG)
- {
- imageAction="Create PNG image from alignment";
- imageTitle=null;
- } else {
- imageAction="Create EPS file from alignment";
- imageTitle=alignFrame.getTitle();
- }
- im = new jalview.util.ImageMaker(this, type, imageAction, width, height, file,
- imageTitle);
if (av.getWrapAlignment())
{
- if (im.getGraphics() != null)
+ height = getWrappedHeight();
+ if (System.getProperty("java.awt.headless") != null
+ && System.getProperty("java.awt.headless").equals("true"))
{
- printWrappedAlignment(im.getGraphics(), width, height, 0);
- im.writeImage();
+ // need to obtain default alignment width and then add in any
+ // additional allowance for id margin
+ // 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);
}
+ else
+ {
+ width = seqPanel.getWidth() + getVisibleIdWidth(false);
+ }
+
}
- else
+ else if (av.getShowAnnotation())
+ {
+ height += annotationPanel.adjustPanelHeight() + 3;
+ }
+
+ try
{
- if (im.getGraphics() != null)
+
+ jalview.util.ImageMaker im;
+ final String imageAction, imageTitle;
+ if (type == jalview.util.ImageMaker.PNG)
+ {
+ imageAction = "Create PNG image from alignment";
+ imageTitle = null;
+ }
+ else
+ {
+ imageAction = "Create EPS file from alignment";
+ imageTitle = alignFrame.getTitle();
+ }
+ im = new jalview.util.ImageMaker(this, type, imageAction, width,
+ height, file, imageTitle);
+ if (av.getWrapAlignment())
+ {
+ if (im.getGraphics() != null)
+ {
+ printWrappedAlignment(im.getGraphics(), width, height, 0);
+ im.writeImage();
+ }
+ }
+ else
{
- printUnwrapped(im.getGraphics(), width, height, 0);
- im.writeImage();
+ if (im.getGraphics() != null)
+ {
+ printUnwrapped(im.getGraphics(), width, height, 0);
+ im.writeImage();
+ }
}
+ } catch (OutOfMemoryError err)
+ {
+ // Be noisy here.
+ System.out.println("########################\n" + "OUT OF MEMORY "
+ + file + "\n" + "########################");
+ new OOMWarning("Creating Image for " + file, err);
+ // System.out.println("Create IMAGE: " + err);
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
}
- } catch (OutOfMemoryError err)
+ } finally
{
- // Be noisy here.
- System.out.println("########################\n" + "OUT OF MEMORY "
- + file + "\n" + "########################");
- new OOMWarning("Creating Image for " + file, err);
- // System.out.println("Create IMAGE: " + err);
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
- finally {
- if (alignFrame!=null)
+ if (alignFrame != null)
{
alignFrame.setProgressBar("Export complete.", progress);
}
{
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;
StringBuffer text = new StringBuffer();
PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
out.println(jalview.io.HTMLOutput.getImageMapHTML());
PaintRefresher.RemoveComponent(this);
if (av != null)
{
- jalview.structure.StructureSelectionManager ssm = av.getStructureSelectionManager();
+ jalview.structure.StructureSelectionManager ssm = av
+ .getStructureSelectionManager();
ssm.removeStructureViewerListener(seqPanel, null);
ssm.removeSelectionListener(seqPanel);
av.setAlignment(null);
{
updateAnnotation(false, false);
}
+
public void updateAnnotation(boolean applyGlobalSettings)
{
- updateAnnotation(applyGlobalSettings,false);
+ updateAnnotation(applyGlobalSettings, false);
}
- public void updateAnnotation(boolean applyGlobalSettings, boolean preserveNewGroupSettings)
+
+ public void updateAnnotation(boolean applyGlobalSettings,
+ boolean preserveNewGroupSettings)
{
- av.updateGroupAnnotationSettings(applyGlobalSettings, preserveNewGroupSettings);
+ av.updateGroupAnnotationSettings(applyGlobalSettings,
+ preserveNewGroupSettings);
adjustAnnotationHeight();
}
/**
* get the name for this view
- * @return
+ *
+ * @return
*/
public String getViewName()
{
/**
* Make/Unmake this alignment panel the current input focus
+ *
* @param b
*/
public void setSelected(boolean b)
{
- try {
+ try
+ {
alignFrame.setSelected(b);
- } catch (Exception ex) {};
-
+ } catch (Exception ex)
+ {
+ }
+ ;
+
if (b)
{
alignFrame.setDisplayedView(this);
- }
+ }
}
@Override
@Override
public void raiseOOMWarning(String string, OutOfMemoryError error)
{
- new OOMWarning(string, error, this);
+ new OOMWarning(string, error, this);
}
public FeatureRenderer cloneFeatureRenderer()
{
-
+
return new FeatureRenderer(this);
}
public void updateFeatureRendererFrom(FeatureRenderer fr)
{
- if (seqPanel.seqCanvas.getFeatureRenderer()!=null) {
+ if (seqPanel.seqCanvas.getFeatureRenderer() != null)
+ {
seqPanel.seqCanvas.getFeatureRenderer().transferSettings(fr);
}
}
git://source.jalview.org / jalview.git / blobdiff