import jalview.api.AlignmentViewPanel;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SearchResults;
+import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
* Highlight the given results on the alignment.
*
*/
- public void highlightSearchResults(SearchResults results)
+ public void highlightSearchResults(SearchResultsI results)
{
scrollToPosition(results);
getSeqPanel().seqCanvas.highlightSearchResults(results);
*
* @param results
*/
- public boolean scrollToPosition(SearchResults results)
+ public boolean scrollToPosition(SearchResultsI results)
{
return scrollToPosition(results, 0, true, false);
}
* @param redrawOverview
* @return
*/
- public boolean scrollToPosition(SearchResults searchResults,
+ public boolean scrollToPosition(SearchResultsI searchResults,
boolean redrawOverview)
{
return scrollToPosition(searchResults, 0, redrawOverview, false);
* if true, try to centre the search results horizontally in the view
* @return false if results were not found
*/
- public boolean scrollToPosition(SearchResults results,
+ public boolean scrollToPosition(SearchResultsI results,
int verticalOffset, boolean redrawOverview, boolean centre)
{
int startv, endv, starts, ends;
}
else
{
- return printUnwrapped(pwidth, pheight, pi, pg);
+ return printUnwrapped(pwidth, pheight, pi, pg, pg);
}
}
* @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;
- }
-
- 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());
+ final int idWidth = getVisibleIdWidth(false);
- // //////////////////////////////////
- // / 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++)
{
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;
}
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;
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();
}
}
* @param verticalOffset
* the number of visible sequences to show above the mapped region
*/
- public void scrollToCentre(SearchResults sr, int verticalOffset)
+ public void scrollToCentre(SearchResultsI sr, int verticalOffset)
{
/*
* To avoid jumpy vertical scrolling (if some sequences are gapped or not
* mapped), we can make the scroll-to location a sequence above the one
* actually mapped.
*/
- SequenceI mappedTo = sr.getResultSequence(0);
+ SequenceI mappedTo = sr.getResults().get(0).getSequence();
List<SequenceI> seqs = av.getAlignment().getSequences();
/*
*/
package jalview.io;
+import jalview.exceptions.NoFileSelectedException;
import jalview.gui.AlignmentPanel;
import jalview.gui.HTMLOptions;
import jalview.gui.OOMWarning;
public class HtmlSvgOutput extends HTMLOutput
{
- private File generatedFile;
public HtmlSvgOutput(AlignmentPanel ap)
{
}
@Override
- public void exportHTML(String file)
+ public void exportHTML(String outputFile)
{
exportStarted();
try
{
- if (file == null)
+ if (outputFile == null)
{
- file = getOutputFile();
+ outputFile = getOutputFile();
}
- generatedFile = new File(file);
+ generatedFile = new File(outputFile);
+ } catch (NoFileSelectedException e)
+ {
+ setProgressMessage(MessageManager.formatMessage(
+ "status.cancelled_image_export_operation", "HTML"));
+ return;
} catch (Exception e)
{
setProgressMessage(MessageManager.formatMessage(
e.printStackTrace();
return;
}
- new Thread()
- {
- @Override
- public void run()
- {
- try
- {
- setProgressMessage(null);
- setProgressMessage(MessageManager.formatMessage(
- "status.exporting_alignment_as_x_file", "HTML"));
- AlignmentDimension aDimension = ap.getAlignmentDimension();
- SVGGraphics2D idPanelGraphics = new SVGGraphics2D(
- aDimension.getWidth(),
- aDimension.getHeight());
- SVGGraphics2D alignPanelGraphics = new SVGGraphics2D(
- aDimension.getWidth(),
- aDimension.getHeight());
-
- String renderStyle = jalview.bin.Cache.getDefault(
- "HTML_RENDERING", "Prompt each time");
-
- // If we need to prompt, and if the GUI is visible then
- // Prompt for rendering style
- if (renderStyle.equalsIgnoreCase("Prompt each time")
- && !isHeadless())
- {
- HTMLOptions svgOption = new HTMLOptions();
- renderStyle = svgOption.getValue();
-
- if (renderStyle == null || svgOption.cancelled)
- {
- setProgressMessage(MessageManager.formatMessage(
- "status.cancelled_image_export_operation", "HTML"));
- return;
- }
- }
-
- if (renderStyle.equalsIgnoreCase("Lineart"))
- {
- idPanelGraphics.setRenderingHint(SVGHints.KEY_DRAW_STRING_TYPE,
- SVGHints.VALUE_DRAW_STRING_TYPE_VECTOR);
- alignPanelGraphics.setRenderingHint(
- SVGHints.KEY_DRAW_STRING_TYPE,
- SVGHints.VALUE_DRAW_STRING_TYPE_VECTOR);
- }
- if (ap.av.getWrapAlignment())
- {
- printWrapped(aDimension.getWidth(), aDimension.getHeight(), 0,
- alignPanelGraphics);
- }
- else
- {
- printUnwrapped(aDimension.getWidth(), aDimension.getHeight(), 0,
- idPanelGraphics, alignPanelGraphics);
- }
-
- String idPanelSvgData = idPanelGraphics.getSVGDocument();
- String alignPanelSvgData = alignPanelGraphics.getSVGDocument();
- String jsonData = getBioJSONData();
- String htmlData = getHtml(idPanelSvgData, alignPanelSvgData, jsonData,
- ap.av.getWrapAlignment());
- FileOutputStream out = new FileOutputStream(generatedFile);
- out.write(htmlData.getBytes());
- out.flush();
- out.close();
- exportCompleted();
- } catch (OutOfMemoryError err)
- {
- System.out.println("########################\n"
- + "OUT OF MEMORY " + generatedFile + "\n"
- + "########################");
- new OOMWarning("Creating Image for " + generatedFile, err);
- } catch (Exception e)
- {
- e.printStackTrace();
- setProgressMessage(MessageManager.formatMessage(
- "info.error_creating_file", "HTML"));
- }
- setProgressMessage(MessageManager.formatMessage(
- "status.export_complete", "HTML"));
- }
- }.start();
-
+ new Thread(this).start();
}
"Hypertext Markup Language");
}
- public int printUnwrapped(int pwidth, int pheight, int pi, Graphics... pg)
+ public int printUnwrapped(int pwidth, int pheight, int pi,
+ Graphics idGraphics, Graphics alignmentGraphics)
throws PrinterException
{
- return ap.printUnwrapped(pwidth, pheight, pi, pg);
+ return ap.printUnwrapped(pwidth, pheight, pi, idGraphics,
+ alignmentGraphics);
}
public int printWrapped(int pwidth, int pheight, int pi, Graphics... pg)
.append(alignmentSvg).append("</div>");
htmlSvg.append("<script language=\"JavaScript\" type=\"text/javascript\" src=\"http://ajax.googleapis.com/ajax/libs/jquery/1/jquery.min.js\"></script>\n"
+ "<script language=\"JavaScript\" type=\"text/javascript\" src=\"http://ajax.googleapis.com/ajax/libs/jqueryui/1.11.2/jquery-ui.min.js\"></script>\n");
}
// javascript for launching file in Jalview
-
htmlSvg.append("<script language=\"JavaScript\">\n");
htmlSvg.append("function openJalviewUsingCurrentUrl(){\n");
htmlSvg.append(" var json = JSON.parse(document.getElementById(\"seqData\").innerHTML);\n");
htmlSvg.append(" document.body.removeChild(myForm);\n");
htmlSvg.append("}\n");
- // jquery facebox for displaying raw BioJSON data");
if (jsonData != null)
{
+ // JQuery FaceBox for displaying raw BioJSON data");
File faceBoxJsFile = new File("examples/javascript/facebox-1.3.js");
try
{
{
return generatedFile;
}
+
+ @Override
+ public void run()
+ {
+ try
+ {
+ setProgressMessage(null);
+ setProgressMessage(MessageManager.formatMessage(
+ "status.exporting_alignment_as_x_file", "HTML"));
+ AlignmentDimension aDimension = ap.getAlignmentDimension();
+ SVGGraphics2D idPanelGraphics = new SVGGraphics2D(
+ aDimension.getWidth(), aDimension.getHeight());
+ SVGGraphics2D alignPanelGraphics = new SVGGraphics2D(
+ aDimension.getWidth(), aDimension.getHeight());
+
+ String renderStyle = jalview.bin.Cache.getDefault("HTML_RENDERING",
+ "Prompt each time");
+
+ // If we need to prompt, and if the GUI is visible then
+ // Prompt for rendering style
+ if (renderStyle.equalsIgnoreCase("Prompt each time") && !isHeadless())
+ {
+ HTMLOptions svgOption = new HTMLOptions();
+ renderStyle = svgOption.getValue();
+
+ if (renderStyle == null || svgOption.cancelled)
+ {
+ setProgressMessage(MessageManager.formatMessage(
+ "status.cancelled_image_export_operation", "HTML"));
+ return;
+ }
+ }
+
+ if (renderStyle.equalsIgnoreCase("Lineart"))
+ {
+ idPanelGraphics.setRenderingHint(SVGHints.KEY_DRAW_STRING_TYPE,
+ SVGHints.VALUE_DRAW_STRING_TYPE_VECTOR);
+ alignPanelGraphics.setRenderingHint(SVGHints.KEY_DRAW_STRING_TYPE,
+ SVGHints.VALUE_DRAW_STRING_TYPE_VECTOR);
+ }
+ if (ap.av.getWrapAlignment())
+ {
+ printWrapped(aDimension.getWidth(), aDimension.getHeight(), 0,
+ alignPanelGraphics);
+ }
+ else
+ {
+ printUnwrapped(aDimension.getWidth(), aDimension.getHeight(), 0,
+ idPanelGraphics, alignPanelGraphics);
+ }
+
+ String idPanelSvgData = idPanelGraphics.getSVGDocument();
+ String alignPanelSvgData = alignPanelGraphics.getSVGDocument();
+ String jsonData = getBioJSONData();
+ String htmlData = getHtml(idPanelSvgData, alignPanelSvgData,
+ jsonData, ap.av.getWrapAlignment());
+ FileOutputStream out = new FileOutputStream(generatedFile);
+ out.write(htmlData.getBytes());
+ out.flush();
+ out.close();
+ setProgressMessage(MessageManager.formatMessage(
+ "status.export_complete", "HTML"));
+ exportCompleted();
+ } catch (OutOfMemoryError err)
+ {
+ System.out.println("########################\n" + "OUT OF MEMORY "
+ + generatedFile + "\n" + "########################");
+ new OOMWarning("Creating Image for " + generatedFile, err);
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ setProgressMessage(MessageManager.formatMessage(
+ "info.error_creating_file", "HTML"));
+ }
+ }
}
git://source.jalview.org / jalview.git / commitdiff