X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=5de14a43272af4839a79231ca98976b92b67128d;hb=fbfbbe26bee37143d5279fe4d254a5a89c96b021;hp=907ff462a39f6d1ad14f5d7874128aa01120bb22;hpb=fd64c343e17a21eb50bcbd1a4e6bf2021a3a81b1;p=jalview.git diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java index 907ff46..5de14a4 100755 --- a/src/jalview/io/AppletFormatAdapter.java +++ b/src/jalview/io/AppletFormatAdapter.java @@ -20,16 +20,20 @@ */ package jalview.io; -import jalview.api.AlignExportSettingI; +import java.util.Locale; + +import jalview.api.AlignExportSettingsI; import jalview.api.AlignmentViewPanel; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; import jalview.datamodel.AlignmentView; +import jalview.datamodel.SeqDistanceContactMatrix; import jalview.datamodel.PDBEntry.Type; import jalview.datamodel.SequenceI; import jalview.ext.jmol.JmolParser; import jalview.structure.StructureImportSettings; +import jalview.util.Platform; import java.io.File; import java.io.IOException; @@ -73,7 +77,9 @@ public class AppletFormatAdapter */ protected String newline = System.getProperty("line.separator"); - private AlignExportSettingI exportSettings; + private AlignExportSettingsI exportSettings; + + private File selectedFile; public static String INVALID_CHARACTERS = "Contains invalid characters"; @@ -85,8 +91,9 @@ public class AppletFormatAdapter public static String getSupportedFormats() { return "Formats currently supported are\n" - + prettyPrint(FileFormats.getInstance().getReadableFormats()); + + prettyPrint(FileFormats.getInstance().getReadableFormats()); } + public AppletFormatAdapter() { } @@ -97,7 +104,7 @@ public class AppletFormatAdapter } public AppletFormatAdapter(AlignmentViewPanel alignPanel, - AlignExportSettingI settings) + AlignExportSettingsI settings) { viewpanel = alignPanel; exportSettings = settings; @@ -146,6 +153,19 @@ public class AppletFormatAdapter public AlignmentI readFile(String file, DataSourceType sourceType, FileFormatI fileFormat) throws IOException { + return readFile(null, file, sourceType, fileFormat); + } + + public AlignmentI readFile(File selectedFile, String file, + DataSourceType sourceType, FileFormatI fileFormat) + throws IOException + { + + this.selectedFile = selectedFile; + if (selectedFile != null) + { + this.inFile = selectedFile.getPath(); + } this.inFile = file; try { @@ -154,37 +174,43 @@ public class AppletFormatAdapter String structureParser = StructureImportSettings .getDefaultPDBFileParser(); boolean isParseWithJMOL = structureParser.equalsIgnoreCase( - StructureImportSettings.StructureParser.JMOL_PARSER - .toString()); + StructureImportSettings.StructureParser.JMOL_PARSER + .toString()); StructureImportSettings.addSettings(annotFromStructure, localSecondaryStruct, serviceSecondaryStruct); if (isParseWithJMOL) { - alignFile = new JmolParser(inFile, sourceType); + // needs a File option + alignFile = new JmolParser( + selectedFile == null ? inFile : selectedFile, sourceType); } else { - // todo is MCview parsing obsolete yet? JAL-2120 + // todo is mc_view parsing obsolete yet? JAL-2120 StructureImportSettings.setShowSeqFeatures(true); - alignFile = new MCview.PDBfile(annotFromStructure, + alignFile = new mc_view.PDBfile(annotFromStructure, localSecondaryStruct, serviceSecondaryStruct, inFile, sourceType); } - ((StructureFile) alignFile).setDbRefType(FileFormat.PDB - .equals(fileFormat) ? Type.PDB : Type.MMCIF); + ((StructureFile) alignFile).setDbRefType( + FileFormat.PDB.equals(fileFormat) ? Type.PDB : Type.MMCIF); + } + else if (selectedFile != null) + { + alignFile = fileFormat + .getReader(new FileParse(selectedFile, sourceType)); } else { // alignFile = fileFormat.getAlignmentFile(inFile, sourceType); - alignFile = fileFormat.getReader(new FileParse(inFile, - sourceType)); + alignFile = fileFormat.getReader(new FileParse(inFile, sourceType)); } return buildAlignmentFromFile(); } catch (Exception e) { e.printStackTrace(); - System.err.println("Failed to read alignment using the '" - + fileFormat + "' reader.\n" + e); + System.err.println("Failed to read alignment using the '" + fileFormat + + "' reader.\n" + e); if (e.getMessage() != null && e.getMessage().startsWith(INVALID_CHARACTERS)) @@ -250,7 +276,7 @@ public class AppletFormatAdapter else { StructureImportSettings.setShowSeqFeatures(true); - alignFile = new MCview.PDBfile(annotFromStructure, + alignFile = new mc_view.PDBfile(annotFromStructure, localSecondaryStruct, serviceSecondaryStruct, source); } ((StructureFile) alignFile).setDbRefType(Type.PDB); @@ -333,10 +359,10 @@ public class AppletFormatAdapter AlignmentViewPanel ap, boolean selectedOnly) { - AlignmentView selvew = ap.getAlignViewport().getAlignmentView( - selectedOnly, false); - AlignmentI aselview = selvew.getVisibleAlignment(ap.getAlignViewport() - .getGapCharacter()); + AlignmentView selvew = ap.getAlignViewport() + .getAlignmentView(selectedOnly, false); + AlignmentI aselview = selvew + .getVisibleAlignment(ap.getAlignViewport().getGapCharacter()); List ala = (ap.getAlignViewport() .getVisibleAlignmentAnnotation(selectedOnly)); if (ala != null) @@ -399,8 +425,7 @@ public class AppletFormatAdapter } catch (Exception e) { System.err.println("Failed to write alignment as a '" - + format.getName() - + "' file\n"); + + format.getName() + "' file\n"); e.printStackTrace(); } @@ -410,19 +435,32 @@ public class AppletFormatAdapter /** * Determines the protocol (i.e DataSourceType.{FILE|PASTE|URL}) for the input * data + * + * BH 2018 allows File or String, and can return RELATIVE_URL * - * @param data + * @param dataObject + * File or String * @return the protocol for the input data */ - public static DataSourceType checkProtocol(String data) + public static DataSourceType checkProtocol(Object dataObject) { + if (dataObject instanceof File) + { + return DataSourceType.FILE; + } + + String data = dataObject.toString(); DataSourceType protocol = DataSourceType.PASTE; - String ft = data.toLowerCase().trim(); + String ft = data.toLowerCase(Locale.ROOT).trim(); if (ft.indexOf("http:") == 0 || ft.indexOf("https:") == 0 || ft.indexOf("file:") == 0) { protocol = DataSourceType.URL; } + else if (Platform.isJS()) + { + protocol = DataSourceType.RELATIVE_URL; + } else if (new File(data).exists()) { protocol = DataSourceType.FILE; @@ -430,6 +468,10 @@ public class AppletFormatAdapter return protocol; } + /** + * @param args + * @j2sIgnore + */ public static void main(String[] args) { int i = 0; @@ -446,10 +488,9 @@ public class AppletFormatAdapter System.gc(); long memf = -r.totalMemory() + r.freeMemory(); long t1 = -System.currentTimeMillis(); - AlignmentI al = afa - .readFile(args[i], DataSourceType.FILE, - new IdentifyFile().identify(args[i], - DataSourceType.FILE)); + AlignmentI al = afa.readFile(args[i], DataSourceType.FILE, + new IdentifyFile().identify(args[i], + DataSourceType.FILE)); t1 += System.currentTimeMillis(); System.gc(); memf += r.totalMemory() - r.freeMemory(); @@ -459,12 +500,12 @@ public class AppletFormatAdapter + " sequences and " + al.getWidth() + " columns."); try { - System.out.println(new AppletFormatAdapter().formatSequences( - FileFormat.Fasta, al, true)); + System.out.println(new AppletFormatAdapter() + .formatSequences(FileFormat.Fasta, al, true)); } catch (Exception e) { - System.err - .println("Couln't format the alignment for output as a FASTA file."); + System.err.println( + "Couln't format the alignment for output as a FASTA file."); e.printStackTrace(System.err); } } @@ -473,8 +514,8 @@ public class AppletFormatAdapter System.out.println("Couldn't read alignment"); } System.out.println("Read took " + (t1 / 1000.0) + " seconds."); - System.out - .println("Difference between free memory now and before is " + System.out.println( + "Difference between free memory now and before is " + (memf / (1024.0 * 1024.0) * 1.0) + " MB"); } catch (Exception e) { @@ -558,8 +599,8 @@ public class AppletFormatAdapter { if (debug) { - System.out.println("Trying to get contents of resource as " - + protocol + ":"); + System.out.println( + "Trying to get contents of resource as " + protocol + ":"); } fp = new FileParse(file, protocol); if (!fp.isValid())