\r
import java.util.*;\r
import javax.swing.*;\r
-import java.io.FileOutputStream;\r
-import org.jibble.epsgraphics.EpsGraphics2D;\r
-import javax.imageio.ImageIO;\r
-import java.awt.image.BufferedImage;\r
import java.awt.print.*;\r
\r
\r
int top;\r
RotatableCanvas rc;\r
AlignViewport av;\r
- SequenceI [] seqs;\r
+ String [] seqstrings;\r
+ SequenceI [] seqs;\r
\r
/**\r
* Creates a new PCAPanel object.\r
\r
boolean sameLength = true;\r
\r
- if ((av.getSelectionGroup() != null) &&\r
- (av.getSelectionGroup().getSize() > 3))\r
+ seqstrings = av.getSelectionAsString();\r
+\r
+ if (av.getSelectionGroup() == null)\r
{\r
- seqs = new Sequence[av.getSelectionGroup().getSize()];\r
- int length = av.getSelectionGroup().getSequenceAt(0).getLength();\r
- for (int i = 0; i < av.getSelectionGroup().getSize(); i++)\r
- {\r
- seqs[i] = av.getSelectionGroup().getSequenceAt(i);\r
- if(seqs[i].getLength()!=length)\r
- {\r
- sameLength = false;\r
- break;\r
- }\r
- }\r
+ seqs = av.alignment.getSequencesArray();\r
}\r
else\r
{\r
- seqs = new Sequence[av.getAlignment().getHeight()];\r
- int length = av.alignment.getSequenceAt(0).getLength();\r
-\r
- for (int i = 0; i < av.getAlignment().getHeight(); i++)\r
- {\r
- seqs[i] = av.getAlignment().getSequenceAt(i);\r
- if(seqs[i].getLength()!=length)\r
- {\r
- sameLength = false;\r
- break;\r
- }\r
-\r
- }\r
+ seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);\r
+ }\r
+\r
+ int length = seqs[0].getLength();\r
+\r
+ for (int i = 0; i < seqs.length; i++)\r
+ {\r
+ if (seqs[i].getLength() != length)\r
+ {\r
+ sameLength = false;\r
+ break;\r
+ }\r
}\r
\r
if (!sameLength)\r
public void run()\r
{\r
try{\r
- pca = new PCA(seqs);\r
+ pca = new PCA(seqstrings);\r
pca.run();\r
\r
// Now find the component coordinates\r
\r
rc.setPoints(points, pca.getM().rows);\r
rc.repaint();\r
- seqs = null;\r
}\r
catch(OutOfMemoryError er)\r
{ JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
printer.start();\r
}\r
\r
+ public void originalSeqData_actionPerformed(ActionEvent e)\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
+ for (int i = 0; i < seqs.length; i++)\r
+ {\r
+ cap.appendText(new jalview.util.Format("%-" + 15 + "s").form(\r
+ seqs[i].getName()));\r
+ cap.appendText(" " + seqstrings[i] + "\n");\r
+\r
+ }\r
+\r
+ Desktop.addInternalFrame(cap, "Original Data",\r
+ 400, 400);\r
+\r
+ }\r
+\r
+\r
\r
class PCAPrinter extends Thread implements Printable\r
{\r
\r
\r
\r
-\r
/**\r
* DOCUMENT ME!\r
*\r
*/\r
public void eps_actionPerformed(ActionEvent e)\r
{\r
- boolean accurateText = true;\r
-\r
- String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",\r
- "Prompt each time");\r
-\r
- // If we need to prompt, and if the GUI is visible then\r
- // Prompt for EPS rendering style\r
- if (renderStyle.equalsIgnoreCase("Prompt each time")\r
- && !\r
- (System.getProperty("java.awt.headless") != null\r
- && System.getProperty("java.awt.headless").equals("true")))\r
- {\r
- EPSOptions eps = new EPSOptions();\r
- renderStyle = eps.getValue();\r
-\r
- if (renderStyle == null || eps.cancelled)\r
- return;\r
-\r
- }\r
-\r
- if (renderStyle.equalsIgnoreCase("text"))\r
- {\r
- accurateText = false;\r
- }\r
-\r
- int width = rc.getWidth();\r
- int height = rc.getHeight();\r
-\r
- try\r
- {\r
- jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(\r
- jalview.bin.Cache.getProperty(\r
- "LAST_DIRECTORY"), new String[]\r
- {"eps"},\r
- new String[]\r
- {"Encapsulated Postscript"},\r
- "Encapsulated Postscript");\r
- chooser.setFileView(new jalview.io.JalviewFileView());\r
- chooser.setDialogTitle("Create EPS file from PCA");\r
- chooser.setToolTipText("Save");\r
-\r
- int value = chooser.showSaveDialog(this);\r
-\r
- if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
- {\r
- return;\r
- }\r
-\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
- chooser.getSelectedFile().getParent());\r
-\r
- FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());\r
- EpsGraphics2D pg = new EpsGraphics2D("PCA", out, 0, 0, width,\r
- height);\r
-\r
- pg.setAccurateTextMode(accurateText);\r
-\r
- rc.drawBackground(pg, rc.bgColour);\r
- rc.drawScene(pg);\r
-\r
- if (rc.drawAxes == true)\r
- {\r
- rc.drawAxes(pg);\r
- }\r
-\r
-\r
- pg.flush();\r
- pg.close();\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
+ makePCAImage(jalview.util.ImageMaker.EPS);\r
}\r
\r
/**\r
*/\r
public void png_actionPerformed(ActionEvent e)\r
{\r
+ makePCAImage(jalview.util.ImageMaker.PNG);\r
+ }\r
+\r
+ void makePCAImage(int type)\r
+ {\r
int width = rc.getWidth();\r
int height = rc.getHeight();\r
\r
- try\r
- {\r
- jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(\r
- jalview.bin.Cache.getProperty(\r
- "LAST_DIRECTORY"), new String[]\r
- {"png"},\r
- new String[]\r
- {"Portable network graphics"},\r
- "Portable network graphics");\r
-\r
- chooser.setFileView(new jalview.io.JalviewFileView());\r
- chooser.setDialogTitle("Create PNG image from PCA");\r
- chooser.setToolTipText("Save");\r
-\r
- int value = chooser.showSaveDialog(this);\r
-\r
- if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
- {\r
- return;\r
- }\r
-\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
- chooser.getSelectedFile().getParent());\r
+ jalview.util.ImageMaker im;\r
\r
- FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());\r
-\r
- BufferedImage bi = new BufferedImage(width, height,\r
- BufferedImage.TYPE_INT_RGB);\r
- Graphics big = bi.getGraphics();\r
-\r
- big.drawImage(rc.img,0,0,this);\r
-\r
- ImageIO.write(bi, "png", out);\r
- out.close();\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
+ if(type == jalview.util.ImageMaker.PNG)\r
+ im = new jalview.util.ImageMaker(this,\r
+ jalview.util.ImageMaker.PNG,\r
+ "Make PNG image from PCA",\r
+ width, height,\r
+ null, null);\r
+ else\r
+ im = new jalview.util.ImageMaker(this,\r
+ jalview.util.ImageMaker.EPS,\r
+ "Make EPS file from PCA",\r
+ width, height,\r
+ null, this.getTitle());\r
+\r
+ if(im.getGraphics()!=null)\r
+ {\r
+ rc.drawBackground(im.getGraphics(), Color.black);\r
+ rc.drawScene(im.getGraphics());\r
+ if (rc.drawAxes == true)\r
+ {\r
+ rc.drawAxes(im.getGraphics());\r
+ }\r
+ im.writeImage();\r
+ }\r
}\r
-\r
}\r