X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=e2cd43a54c7e5f725299a494081c956ce18aca2a;hb=f29fd62aa198553b53e43a14549611832d2706b3;hp=41fac7fb66899d083c1318f6126ae4d151fc4169;hpb=fe72160257543fca39f7959fc1347665e95764a2;p=jalview.git diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java index 41fac7f..e2cd43a 100755 --- a/src/jalview/io/AppletFormatAdapter.java +++ b/src/jalview/io/AppletFormatAdapter.java @@ -20,6 +20,10 @@ */ package jalview.io; +import java.io.File; +import java.io.InputStream; +import java.util.List; + import jalview.api.AlignViewportI; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentAnnotation; @@ -28,10 +32,6 @@ import jalview.datamodel.AlignmentView; import jalview.datamodel.SequenceGroup; import jalview.util.MessageManager; -import java.io.File; -import java.io.InputStream; -import java.util.List; - /** * A low level class for alignment and feature IO with alignment formatting * methods used by both applet and application for generating flat alignment @@ -43,6 +43,40 @@ import java.util.List; */ public class AppletFormatAdapter { + private AlignViewportI viewport; + + public static String FILE = "File"; + + public static String URL = "URL"; + + public static String PASTE = "Paste"; + + public static String CLASSLOADER = "ClassLoader"; + + /** + * add jalview-derived non-secondary structure annotation from PDB structure + */ + boolean annotFromStructure = false; + + /** + * add secondary structure from PDB data with built-in algorithms + */ + boolean localSecondaryStruct = false; + + /** + * process PDB data with web services + */ + boolean serviceSecondaryStruct = false; + + private AlignFile alignFile = null; + + String inFile; + + /** + * character used to write newlines + */ + protected String newline = System.getProperty("line.separator"); + /** * List of valid format strings used in the isValidFormat method */ @@ -99,6 +133,15 @@ public class AppletFormatAdapter public static String SUPPORTED_FORMATS = "Formats currently supported are\n" + prettyPrint(READABLE_FORMATS); + public AppletFormatAdapter() + { + } + + public AppletFormatAdapter(AlignViewportI viewport) + { + this.viewport = viewport; + } + /** * * @param els @@ -116,37 +159,6 @@ public class AppletFormatAdapter return list.toString(); } - public static String FILE = "File"; - - public static String URL = "URL"; - - public static String PASTE = "Paste"; - - public static String CLASSLOADER = "ClassLoader"; - - /** - * add jalview-derived non-secondary structure annotation from PDB structure - */ - boolean annotFromStructure = false; - - /** - * add secondary structure from PDB data with built-in algorithms - */ - boolean localSecondaryStruct = false; - - /** - * process PDB data with web services - */ - boolean serviceSecondaryStruct = false; - - AlignFile afile = null; - - String inFile; - - /** - * character used to write newlines - */ - protected String newline = System.getProperty("line.separator"); public void setNewlineString(String nl) { @@ -220,73 +232,75 @@ public class AppletFormatAdapter Alignment al; if (format.equals("FASTA")) { - afile = new FastaFile(inFile, type); + alignFile = new FastaFile(inFile, type); } else if (format.equals("MSF")) { - afile = new MSFfile(inFile, type); + alignFile = new MSFfile(inFile, type); } else if (format.equals("PileUp")) { - afile = new PileUpfile(inFile, type); + alignFile = new PileUpfile(inFile, type); } else if (format.equals("CLUSTAL")) { - afile = new ClustalFile(inFile, type); + alignFile = new ClustalFile(inFile, type); } else if (format.equals("BLC")) { - afile = new BLCFile(inFile, type); + alignFile = new BLCFile(inFile, type); } else if (format.equals("PIR")) { - afile = new PIRFile(inFile, type); + alignFile = new PIRFile(inFile, type); } else if (format.equals("PFAM")) { - afile = new PfamFile(inFile, type); + alignFile = new PfamFile(inFile, type); } else if (format.equals("JnetFile")) { - afile = new JPredFile(inFile, type); - ((JPredFile) afile).removeNonSequences(); + alignFile = new JPredFile(inFile, type); + ((JPredFile) alignFile).removeNonSequences(); } else if (format.equals("PDB")) { - afile = new MCview.PDBfile(annotFromStructure, + alignFile = new MCview.PDBfile(annotFromStructure, localSecondaryStruct, serviceSecondaryStruct, inFile, type); // Uncomment to test Jmol data based PDB processing: JAL-1213 // afile = new jalview.ext.jmol.PDBFileWithJmol(inFile, type); } else if (format.equals("STH")) { - afile = new StockholmFile(inFile, type); + alignFile = new StockholmFile(inFile, type); } else if (format.equals("SimpleBLAST")) { - afile = new SimpleBlastFile(inFile, type); + alignFile = new SimpleBlastFile(inFile, type); } else if (format.equals(PhylipFile.FILE_DESC)) { - afile = new PhylipFile(inFile, type); + alignFile = new PhylipFile(inFile, type); } else if (format.equals(JSONFile.FILE_DESC)) { - afile = new JSONFile(inFile, type); - al = new Alignment(afile.getSeqsAsArray()); - afile.addAnnotations(al); - for (SequenceGroup sg : afile.getSeqGroups()) + alignFile = new JSONFile(inFile, type); + al = new Alignment(alignFile.getSeqsAsArray()); + alignFile.addAnnotations(al); + ((JSONFile) alignFile).setViewport(viewport); + for (SequenceGroup sg : alignFile.getSeqGroups()) { al.addGroup(sg); } + return al; } else if (format.equals(HtmlFile.FILE_DESC)) { - afile = new HtmlFile(inFile, type); - al = new Alignment(afile.getSeqsAsArray()); - afile.addAnnotations(al); - for (SequenceGroup sg : afile.getSeqGroups()) + alignFile = new HtmlFile(inFile, type); + al = new Alignment(alignFile.getSeqsAsArray()); + alignFile.addAnnotations(al); + for (SequenceGroup sg : alignFile.getSeqGroups()) { al.addGroup(sg); } @@ -294,12 +308,12 @@ public class AppletFormatAdapter } else if (format.equals("RNAML")) { - afile = new RnamlFile(inFile, type); + alignFile = new RnamlFile(inFile, type); } - al = new Alignment(afile.getSeqsAsArray()); + al = new Alignment(alignFile.getSeqsAsArray()); - afile.addAnnotations(al); + alignFile.addAnnotations(al); return al; } catch (Exception e) @@ -320,11 +334,11 @@ public class AppletFormatAdapter try { // Possible sequence is just residues with no label - afile = new FastaFile(">UNKNOWN\n" + inFile, "Paste"); - Alignment al = new Alignment(afile.getSeqsAsArray()); + alignFile = new FastaFile(">UNKNOWN\n" + inFile, "Paste"); + Alignment al = new Alignment(alignFile.getSeqsAsArray()); - afile.addSeqGroups(al); - afile.addAnnotations(al); + alignFile.addSeqGroups(al); + alignFile.addAnnotations(al); return al; } catch (Exception ex) @@ -367,72 +381,73 @@ public class AppletFormatAdapter Alignment al; if (format.equals("FASTA")) { - afile = new FastaFile(source); + alignFile = new FastaFile(source); } else if (format.equals("MSF")) { - afile = new MSFfile(source); + alignFile = new MSFfile(source); } else if (format.equals("PileUp")) { - afile = new PileUpfile(source); + alignFile = new PileUpfile(source); } else if (format.equals("CLUSTAL")) { - afile = new ClustalFile(source); + alignFile = new ClustalFile(source); } else if (format.equals("BLC")) { - afile = new BLCFile(source); + alignFile = new BLCFile(source); } else if (format.equals("PIR")) { - afile = new PIRFile(source); + alignFile = new PIRFile(source); } else if (format.equals("PFAM")) { - afile = new PfamFile(source); + alignFile = new PfamFile(source); } else if (format.equals("JnetFile")) { - afile = new JPredFile(source); - ((JPredFile) afile).removeNonSequences(); + alignFile = new JPredFile(source); + ((JPredFile) alignFile).removeNonSequences(); } else if (format.equals("PDB")) { - afile = new MCview.PDBfile(annotFromStructure, + alignFile = new MCview.PDBfile(annotFromStructure, localSecondaryStruct, serviceSecondaryStruct, source); } else if (format.equals("STH")) { - afile = new StockholmFile(source); + alignFile = new StockholmFile(source); } else if (format.equals("RNAML")) { - afile = new RnamlFile(source); + alignFile = new RnamlFile(source); } else if (format.equals("SimpleBLAST")) { - afile = new SimpleBlastFile(source); + alignFile = new SimpleBlastFile(source); } else if (format.equals(PhylipFile.FILE_DESC)) { - afile = new PhylipFile(source); + alignFile = new PhylipFile(source); } else if (format.equals(JSONFile.FILE_DESC)) { - afile = new JSONFile(source); - al = new Alignment(afile.getSeqsAsArray()); - afile.addAnnotations(al); - afile.addSeqGroups(al); + alignFile = new JSONFile(source); + // ((JSONFile) afile).setViewport(viewport); + al = new Alignment(alignFile.getSeqsAsArray()); + alignFile.addAnnotations(al); + alignFile.addSeqGroups(al); return al; } else if (format.equals(HtmlFile.FILE_DESC)) { - afile = new HtmlFile(source); + alignFile = new HtmlFile(source); } - al = new Alignment(afile.getSeqsAsArray()); - afile.addAnnotations(al); + al = new Alignment(alignFile.getSeqsAsArray()); + alignFile.addAnnotations(al); return al; } catch (Exception e) @@ -453,10 +468,10 @@ public class AppletFormatAdapter try { // Possible sequence is just residues with no label - afile = new FastaFile(">UNKNOWN\n" + inFile, "Paste"); - Alignment al = new Alignment(afile.getSeqsAsArray()); - afile.addAnnotations(al); - afile.addSeqGroups(al); + alignFile = new FastaFile(">UNKNOWN\n" + inFile, "Paste"); + Alignment al = new Alignment(alignFile.getSeqsAsArray()); + alignFile.addAnnotations(al); + alignFile.addSeqGroups(al); return al; } catch (Exception ex) @@ -568,6 +583,7 @@ public class AppletFormatAdapter else if (format.equalsIgnoreCase(JSONFile.FILE_DESC)) { afile = new JSONFile(); + afile.setViewport(viewport); // Add groups to AlignFile afile.seqGroups = alignment.getGroups(); @@ -857,4 +873,14 @@ public class AppletFormatAdapter } return null; } + + public AlignFile getAlignFile() + { + return alignFile; + } + + public void setAlignFile(AlignFile alignFile) + { + this.alignFile = alignFile; + } }