test alignment annotation file IO for example given in documentation and for multiple combine statement
--- /dev/null
+#Comment lines follow the hash symbol
+JALVIEW_ANNOTATION
+SEQUENCE_REF FER1_MESCR 5
+BAR_GRAPH Bar Graph 1 <html>an <em>html tooltip</em> for Bar graph 1.</html> ||-100,-|-200,-|-300,-|-400,-|200,+|300,+|150,+
+LINE_GRAPH Green Values 1.1|2.2|1.3|3.4|0.7|1.4|3.3|2.2|2.1|-1.1|3.2
+LINE_GRAPH Red Values 2.1|3.2|1.3|-1.4|5.5|1.4|1.3|4.2|-1.1|1.1|3.2
+BAR_GRAPH Bar Graph 2 1,.|2,*|3,:|4,.|5,*|4,:|3,.|2|1|1|2|3|4|5|4
+NO_GRAPH Icons ||||E,Sheet1|E|E||||H,Sheet 2|H|H|H||||||
+NO_GRAPH Purple Letters m|y|p|r|o|t|e|i|n
+COLOUR Bar Graph 2 blue
+COLOUR Red Values 255,0,0
+COLOUR Green Values green
+COLOUR Purple Letters 151,52,228
+COMBINE Green Values Red Values
+GRAPHLINE Red Values 2.6 threshold black
+
+SEQUENCE_GROUP Group_A 30 50 *
+SEQUENCE_GROUP Group_B 1 351 2-5
+SEQUENCE_GROUP Group_C 12 14 -1 seq1 seq2 seq3
+PROPERTIES Group_A description=This is the description colour=Helix Propensity pidThreshold=0 outlineColour=red displayBoxes=true displayText=false colourText=false textCol1=black textCol2=black textColThreshold=0
+PROPERTIES Group_B outlineColour=red
+PROPERTIES Group_C colour=Clustal
--- /dev/null
+#Comment lines follow the hash symbol
+JALVIEW_ANNOTATION
+SEQUENCE_REF FER1_MESCR 5
+BAR_GRAPH Bar Graph 1 <html>an <em>html tooltip</em> for Bar graph 1.</html> ||-100,-|-200,-|-300,-|-400,-|200,+|300,+|150,+
+LINE_GRAPH Green Values 1.1|2.2|1.3|3.4|0.7|1.4|3.3|2.2|2.1|-1.1|3.2
+LINE_GRAPH Red Values 2.1|3.2|1.3|-1.4|5.5|1.4|1.3|4.2|-1.1|1.1|3.2
+LINE_GRAPH Blue Values 0|0|0|1.1|2.2|1.3|3.4|0.7|1.4|3.3|2.2
+LINE_GRAPH Yellow Values 3.0|3.0|3.0|2.1|3.2|1.3|-1.4|5.5|1.4|1.3|4.2
+
+BAR_GRAPH Bar Graph 2 1,.|2,*|3,:|4,.|5,*|4,:|3,.|2|1|1|2|3|4|5|4
+
+NO_GRAPH Icons ||||E,Sheet1|E|E||||H,Sheet 2|H|H|H||||||
+NO_GRAPH Purple Letters m|y|p|r|o|t|e|i|n
+COLOUR Bar Graph 2 blue
+COLOUR Red Values 255,0,0
+COLOUR Green Values green
+COLOUR Blue Values blue
+COLOUR Yellow Values yellow
+COLOUR Purple Letters 151,52,228
+
+COMBINE Green Values Red Values
+COMBINE Blue Values Yellow Values
+
+GRAPHLINE Red Values 2.6 threshold black
+
+SEQUENCE_GROUP Group_A 30 50 *
+SEQUENCE_GROUP Group_B 1 351 2-5
+SEQUENCE_GROUP Group_C 12 14 -1 seq1 seq2 seq3
+PROPERTIES Group_A description=This is the description colour=Helix Propensity pidThreshold=0 outlineColour=red displayBoxes=true displayText=false colourText=false textCol1=black textCol2=black textColThreshold=0
+PROPERTIES Group_B outlineColour=red
+PROPERTIES Group_C colour=Clustal
--- /dev/null
+package jalview.io;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+import jalview.datamodel.AlignmentI;
+
+import java.io.File;
+
+import org.junit.Test;
+
+public class AnnotationFileIOTest
+{
+
+ static String TestFiles[][] = {{ "Test example annotation import/export","examples/uniref50.fa", "examples/testdata/example_annot_file.jva" }
+ ,{"Test multiple combine annotation statements import/export","examples/uniref50.fa", "examples/testdata/test_combine_annot.jva"}};
+
+ @Test
+ public void exampleAnnotationFileIO() throws Exception
+ {
+ for (String[] testPair:TestFiles)
+ {
+ testAnnotationFileIO(testPair[0], new File(testPair[1]), new File(testPair[2]));
+ }
+ }
+
+ public static AlignmentI readAlignmentFile(File f)
+ {
+ System.out.println("Reading file: " + f);
+ String ff = f.getPath();
+ try
+ {
+ FormatAdapter rf = new FormatAdapter();
+
+ AlignmentI al = rf.readFile(ff, AppletFormatAdapter.FILE,
+ new IdentifyFile().Identify(ff, AppletFormatAdapter.FILE));
+
+ // make sure dataset is initialised ? not sure about this
+ for (int i = 0; i < al.getSequencesArray().length; ++i)
+ {
+ al.getSequenceAt(i).setDatasetSequence(al.getSequenceAt(i).createDatasetSequence());
+ }
+ assertNotNull("Couldn't read supplied alignment data.", al);
+ return al;
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ fail("Couln't read the alignment in file '"+f.toString()+"'");
+ return null;
+ }
+ /**
+ * test alignment data in given file can be imported, exported and reimported
+ * with no dataloss
+ *
+ * @param f
+ * - source datafile (IdentifyFile.identify() should work with it)
+ * @param ioformat
+ * - label for IO class used to write and read back in the data from
+ * f
+ */
+ public static void testAnnotationFileIO(String testname, File f, File annotFile)
+ {
+ System.out.println("Test: "+testname+"\nReading annotation file '"+annotFile+"' onto : " + f);
+ String af = annotFile.getPath();
+ try
+ {
+ AlignmentI al = readAlignmentFile(f);
+
+ assertTrue("Test "+testname+"\nAlignment was not annotated - annotation file not imported.",new AnnotationFile().readAnnotationFile(al, af, FormatAdapter.FILE));
+
+ String anfileout = new AnnotationFile().printAnnotations(al.getAlignmentAnnotation(), al.getGroups(), al.getProperties());
+ assertTrue("Test "+testname+"\nAlignment annotation file was not regenerated. Null string",anfileout!=null);
+ assertTrue("Test "+testname+"\nAlignment annotation file was not regenerated. Empty string",anfileout.length()>"JALVIEW_ANNOTATION".length());
+
+ System.out.println("Output annotation file:\n"+anfileout+"\n<<EOF\n");
+
+ AlignmentI al_new = readAlignmentFile(f);
+ assertTrue("Test "+testname+"\nregenerated annotation file did not annotate alignment.",new AnnotationFile().readAnnotationFile(al_new, anfileout, FormatAdapter.PASTE));
+
+ // test for consistency in io
+ StockholmFileTest.testAlignmentEquivalence(al, al_new);
+ return;
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ fail("Test "+testname+"\nCouldn't complete Annotation file roundtrip input/output/input test for '"+annotFile+"'.");
+ }
+}
git://source.jalview.org / jalview.git / commitdiff