X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=examples%2Fgroovy%2FJvLoadTester.groovy;h=cc92e4060dc40d5a424ab99493f9aeebfe3022ee;hb=HEAD;hp=d944ece29d449cc100863c74ef09c3704ca7b610;hpb=723d0cff35b408c12fc13b44ff50193c588d6ff1;p=jalview.git

diff --git a/examples/groovy/JvLoadTester.groovy b/examples/groovy/JvLoadTester.groovy
index d944ece..cc92e40 100644
--- a/examples/groovy/JvLoadTester.groovy
+++ b/examples/groovy/JvLoadTester.groovy
@@ -1,138 +1,158 @@
-import jalview.gui.*;
-import jalview.io.*;
-
-def class JvLoadTest {
-    FileLoader fl = null;
-    def String safename = null;
-    JvLoadTest(String sname) { 
-	if (!new File(sname).exists() || new File(sname).canWrite())
-	    {
-		safename = sname;
-	    } else {
-		System.err.println("Warning : "+sname+" isn't being used to store temporary files.");
-	    }	
-    }
-    def public boolean doTest (file) {
-	fl = new FileLoader(false);
-	System.gc();
-	AlignFrame af = fl.LoadFileWaitTillLoaded(file
-						  ,FormatAdapter.FILE);
-	return doTest(af);
-    }
-    def public boolean doSequentialReadTest (file) {
-	return doSequentialReadTest(file, 0);
-    }
-    // Return true if there is more data to read.
-    def public boolean peekFp(FileParse fp) {
-	try { fp.mark(); }  catch (Exception ex) { System.err.println("FAILED mark."+ex); return false; };
-	try {
-	  def String nl;
-	  for (i in 1..3) { 
-	   nl = fp.nextLine();
-	   if (nl==null) { return false; }
-	   System.out.println(nl +"\\n");
-          }
-	} catch (Exception e) { // end of file.
-		return false; };
-	try { fp.reset(); } catch (Exception ex) { System.err.println("FAILED rewind."+ex); return false; };
-	return true;
-    }
-    /*
-      Halt after loading the mx'th entry in the filestream
-    */
-    def public boolean doSequentialReadTest (file, int mx) {
-	// first properly open the file
-	//	if (!doTest(file)) { return };
-	def FileParse fp = null;
-	try {
-		fp = new FileParse(file, AppletFormatAdapter.FILE);
-	} catch (Exception e) { System.err.println("Couldn't open "+file+"\\n"); e.printStackTrace(); return false;};
-	Desktop.instance.closeAll_actionPerformed(null)
-	    System.gc();
-	while (fp!=null && fp.isValid() && (mx==0 || mx!=fp.index)) {
-	    if (!peekFp(fp)) return false;
-	    fl = new FileLoader(false);
-	    AlignFrame af = fl.LoadFileWaitTillLoaded(fp, null);
-	    System.out.println("FileParse index: "+fp.index);	
-	    if (af!=null && (mx==0 || mx!=fp.index))
-		{	def boolean res = doTest(af);
-		if (!res)
-		    {
-			// return false;
-		    }
-		} else {
-		    // return false;
-		}
-	}
-	return true;
-    }
-    def public void waitTillSettled(AlignFrame af)
-    {
-	if (af==null) { return; }
-	Thread.sleep(10);
-	while (af.getViewport().updatingConsensus || af.getViewport().updatingConservation) {
-	    Thread.sleep(150); // wait until things settle down
-	}
-    }
-    def public boolean doTest(AlignFrame af) {
-	Object pr = af.getViewport().getAlignment().getProperty("AC");
-	if (pr!=null) { System.out.println("Accession = "+(String) pr); }
-	af.selectAllSequenceMenuItem_actionPerformed(null)
-	    def boolean done = false;
-	// Just try to save - don\'t mess around with clipboard
-	/*while (!done) {
-	  try {
-	  af.copy_actionPerformed(null)
-	  done = true;
-	  } catch (Exception e) {
-	  Thread.sleep(100); // wait until clipboard might be available again
-	  }
-	  }*/
-	if (af==null) { return false; }
-	waitTillSettled(af);
-	// Try and save as a jalview project and reload
-	try {
-	    //	    af.saveAlignment(safename, "Jalview")
-	    new Jalview2XML().SaveState(new java.io.File(safename));
-	    Thread.sleep(100);
-		} catch (Exception ex) { 
-		    System.out.println("Couldn\'t save.");
-		    ex.printStackTrace(System.err);
-		    return false;
-		}
-	waitTillSettled(af);
-	try {
-	    Desktop.instance.closeAll_actionPerformed(null);
-	} catch (Exception ex) {}
-	System.gc();
-	try {
-	    af = new FileLoader(false).LoadFileWaitTillLoaded(safename, FormatAdapter.FILE);	
-	} 
-	catch (Exception ex) {
-	    System.out.println("Couldn't reload saved file.");
-            System.gc();
-	    return false;
-	}
-	waitTillSettled(af);
-
-	Desktop.instance.closeAll_actionPerformed(null);
-
-	// af.paste(true)
-	// af.newView_actionPerformed(null)
-	// af.newView_actionPerformed(null)
-
-	return true;
-    }
-    def public boolean TestForAll(String dir) {
-	println "For directory or file : "+dir;
-	File fd = new File(dir);
-	if (!fd.isDirectory()) { return doSequentialReadTest(dir); }
-	fd.eachFile() { file -> TestForAll(file.getAbsolutePath()) };
-    }
-}
-def JvLoadTest newJvLoadTest(String tempFile) {
-	jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
-	System.gc();
-	jalview.gui.Desktop.instance.desktop.showMemoryUsage(true);
-	return new JvLoadTest(tempFile)
-}
\ No newline at end of file
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+import jalview.gui.*;
+import jalview.io.*;
+
+class JvLoadTest {
+    FileLoader fl = null;
+    def String safename = null;
+    JvLoadTest(String sname) { 
+	if (!new File(sname).exists() || new File(sname).canWrite())
+	    {
+		safename = sname;
+	    } else {
+		System.err.println("Warning : "+sname+" isn't being used to store temporary files.");
+	    }	
+    }
+    def public boolean doTest (file) {
+	fl = new FileLoader(false);
+	System.gc();
+	AlignFrame af = fl.LoadFileWaitTillLoaded(file
+						  ,FormatAdapter.FILE);
+	return doTest(af);
+    }
+    def public boolean doSequentialReadTest (file) {
+	return doSequentialReadTest(file, 0);
+    }
+    // Return true if there is more data to read.
+    def public boolean peekFp(FileParse fp) {
+	try { fp.mark(); }  catch (Exception ex) { System.err.println("FAILED mark."+ex); return false; };
+	try {
+	  def String nl;
+	  for (i in 1..3) { 
+	   nl = fp.nextLine();
+	   if (nl==null) { return false; }
+	   System.out.println(nl +"\\n");
+          }
+	} catch (Exception e) { // end of file.
+		return false; };
+	try { fp.reset(); } catch (Exception ex) { System.err.println("FAILED rewind."+ex); return false; };
+	return true;
+    }
+    /*
+      Halt after loading the mx'th entry in the filestream
+    */
+    def public boolean doSequentialReadTest (file, int mx) {
+	// first properly open the file
+	//	if (!doTest(file)) { return };
+	def FileParse fp = null;
+	try {
+		fp = new FileParse(file, AppletFormatAdapter.FILE);
+	} catch (Exception e) { System.err.println("Couldn't open "+file+"\\n"); e.printStackTrace(); return false;};
+	Desktop.instance.closeAll_actionPerformed(null)
+	    System.gc();
+	while (fp!=null && fp.isValid() && (mx==0 || mx!=fp.index)) {
+	    if (!peekFp(fp)) return false;
+	    fl = new FileLoader(false);
+	    AlignFrame af = fl.LoadFileWaitTillLoaded(fp, null);
+	    System.out.println("FileParse index: "+fp.index);	
+	    if (af!=null && (mx==0 || mx!=fp.index))
+		{	def boolean res = doTest(af);
+		if (!res)
+		    {
+			// return false;
+		    }
+		} else {
+		    // return false;
+		}
+	}
+	return true;
+    }
+    def public void waitTillSettled(AlignFrame af)
+    {
+	if (af==null) { return; }
+	Thread.sleep(10);
+	while (af.getViewport().updatingConsensus || af.getViewport().updatingConservation) {
+	    Thread.sleep(150); // wait until things settle down
+	}
+    }
+    def public boolean doTest(AlignFrame af) {
+	Object pr = af.getViewport().getAlignment().getProperty("AC");
+	if (pr!=null) { System.out.println("Accession = "+(String) pr); }
+	af.selectAllSequenceMenuItem_actionPerformed(null)
+	    def boolean done = false;
+	// Just try to save - don\'t mess around with clipboard
+	/*while (!done) {
+	  try {
+	  af.copy_actionPerformed(null)
+	  done = true;
+	  } catch (Exception e) {
+	  Thread.sleep(100); // wait until clipboard might be available again
+	  }
+	  }*/
+	if (af==null) { return false; }
+	waitTillSettled(af);
+	// Try and save as a jalview project and reload
+	try {
+	    //	    af.saveAlignment(safename, "Jalview")
+	    new Jalview2XML().SaveState(new java.io.File(safename));
+	    Thread.sleep(100);
+		} catch (Exception ex) { 
+		    System.out.println("Couldn\'t save.");
+		    ex.printStackTrace(System.err);
+		    return false;
+		}
+	waitTillSettled(af);
+	try {
+	    Desktop.instance.closeAll_actionPerformed(null);
+	} catch (Exception ex) {}
+	System.gc();
+	try {
+	    af = new FileLoader(false).LoadFileWaitTillLoaded(safename, FormatAdapter.FILE);	
+	} 
+	catch (Exception ex) {
+	    System.out.println("Couldn't reload saved file.");
+            System.gc();
+	    return false;
+	}
+	waitTillSettled(af);
+
+	Desktop.instance.closeAll_actionPerformed(null);
+
+	// af.paste(true)
+	// af.newView_actionPerformed(null)
+	// af.newView_actionPerformed(null)
+
+	return true;
+    }
+    def public boolean TestForAll(String dir) {
+	println "For directory or file : "+dir;
+	File fd = new File(dir);
+	if (!fd.isDirectory()) { return doSequentialReadTest(dir); }
+	fd.eachFile() { file -> TestForAll(file.getAbsolutePath()) };
+    }
+}
+def JvLoadTest newJvLoadTest(String tempFile) {
+	jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
+	System.gc();
+	jalview.gui.Desktop.instance.desktop.showMemoryUsage(true);
+	return new JvLoadTest(tempFile)
+}