X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=56e9fa10ada182f95b7bcbb45b4a0c8c39dbde43;hb=8a2a0cda7067530f8481c2aec203e18d555f2dfd;hp=95cbb6128a4619117cc92b542f684627b3caa04e;hpb=c9a98f3738fa773afd01ea5d5881b604855fa1b8;p=jalview.git diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java index 95cbb61..56e9fa1 100755 --- a/src/jalview/io/AppletFormatAdapter.java +++ b/src/jalview/io/AppletFormatAdapter.java @@ -20,6 +20,12 @@ */ package jalview.io; +import java.io.File; +import java.io.IOException; +import java.io.InputStream; +import java.util.List; +import java.util.Locale; + import jalview.api.AlignExportSettingsI; import jalview.api.AlignmentViewPanel; import jalview.datamodel.Alignment; @@ -30,11 +36,7 @@ import jalview.datamodel.PDBEntry.Type; import jalview.datamodel.SequenceI; import jalview.ext.jmol.JmolParser; import jalview.structure.StructureImportSettings; - -import java.io.File; -import java.io.IOException; -import java.io.InputStream; -import java.util.List; +import jalview.util.Platform; /** * A low level class for alignment and feature IO with alignment formatting @@ -151,15 +153,21 @@ public class AppletFormatAdapter { return readFile(null, file, sourceType, fileFormat); } - - public AlignmentI readFile(File selectedFile, String file, DataSourceType sourceType, - FileFormatI fileFormat) throws IOException + + public AlignmentI readFile(File selectedFile, String file, + DataSourceType sourceType, FileFormatI fileFormat) + throws IOException + { + return readFile(selectedFile, file, sourceType, fileFormat, null); + } + + public AlignmentI readFile(File selectedFile, String file, + DataSourceType sourceType, FileFormatI fileFormat, + StructureImportSettings.TFType tempfacType) throws IOException { this.selectedFile = selectedFile; - if (selectedFile != null) - this.inFile = selectedFile.getPath(); - this.inFile = file; + this.inFile = selectedFile != null ? selectedFile.getPath() : file; try { if (fileFormat.isStructureFile()) @@ -171,25 +179,34 @@ public class AppletFormatAdapter .toString()); StructureImportSettings.addSettings(annotFromStructure, localSecondaryStruct, serviceSecondaryStruct); + if (tempfacType != null) + { + StructureImportSettings.setTemperatureFactorType(tempfacType); + } if (isParseWithJMOL) { // needs a File option - alignFile = new JmolParser(selectedFile == null ? inFile : selectedFile, sourceType); + alignFile = new JmolParser( + selectedFile == null ? inFile : selectedFile, sourceType, + StructureImportSettings.getTemperatureFactorType()); } 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); } - else if (selectedFile != null) { - alignFile = fileFormat.getReader(new FileParse(selectedFile, sourceType)); - } else + else if (selectedFile != null) + { + alignFile = fileFormat + .getReader(new FileParse(selectedFile, sourceType)); + } + else { // alignFile = fileFormat.getAlignmentFile(inFile, sourceType); alignFile = fileFormat.getReader(new FileParse(inFile, sourceType)); @@ -198,7 +215,7 @@ public class AppletFormatAdapter } catch (Exception e) { e.printStackTrace(); - System.err.println("Failed to read alignment using the '" + fileFormat + jalview.bin.Console.errPrintln("Failed to read alignment using the '" + fileFormat + "' reader.\n" + e); if (e.getMessage() != null @@ -265,7 +282,7 @@ 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); @@ -280,7 +297,7 @@ public class AppletFormatAdapter } catch (Exception e) { e.printStackTrace(); - System.err.println("Failed to read alignment using the '" + format + jalview.bin.Console.errPrintln("Failed to read alignment using the '" + format + "' reader.\n" + e); if (e.getMessage() != null @@ -407,13 +424,13 @@ public class AppletFormatAdapter String afileresp = afile.print(seqs, jvsuffix); if (afile.hasWarningMessage()) { - System.err.println("Warning raised when writing as " + format + jalview.bin.Console.errPrintln("Warning raised when writing as " + format + " : " + afile.getWarningMessage()); } return afileresp; } catch (Exception e) { - System.err.println("Failed to write alignment as a '" + jalview.bin.Console.errPrintln("Failed to write alignment as a '" + format.getName() + "' file\n"); e.printStackTrace(); } @@ -421,30 +438,32 @@ public class AppletFormatAdapter return null; } - /** * 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 dataObject File or String + * @param dataObject + * File or String * @return the protocol for the input data */ public static DataSourceType checkProtocol(Object dataObject) { - if(dataObject instanceof File) + 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 (jalview.bin.Jalview.isJS()) + else if (Platform.isJS()) { protocol = DataSourceType.RELATIVE_URL; } @@ -455,6 +474,10 @@ public class AppletFormatAdapter return protocol; } + /** + * @param args + * @j2sIgnore + */ public static void main(String[] args) { int i = 0; @@ -465,7 +488,7 @@ public class AppletFormatAdapter { try { - System.out.println("Reading file: " + f); + jalview.bin.Console.outPrintln("Reading file: " + f); AppletFormatAdapter afa = new AppletFormatAdapter(); Runtime r = Runtime.getRuntime(); System.gc(); @@ -479,36 +502,36 @@ public class AppletFormatAdapter memf += r.totalMemory() - r.freeMemory(); if (al != null) { - System.out.println("Alignment contains " + al.getHeight() + jalview.bin.Console.outPrintln("Alignment contains " + al.getHeight() + " sequences and " + al.getWidth() + " columns."); try { - System.out.println(new AppletFormatAdapter() + jalview.bin.Console.outPrintln(new AppletFormatAdapter() .formatSequences(FileFormat.Fasta, al, true)); } catch (Exception e) { - System.err.println( + jalview.bin.Console.errPrintln( "Couln't format the alignment for output as a FASTA file."); e.printStackTrace(System.err); } } else { - System.out.println("Couldn't read alignment"); + jalview.bin.Console.outPrintln("Couldn't read alignment"); } - System.out.println("Read took " + (t1 / 1000.0) + " seconds."); - System.out.println( + jalview.bin.Console.outPrintln("Read took " + (t1 / 1000.0) + " seconds."); + jalview.bin.Console.outPrintln( "Difference between free memory now and before is " + (memf / (1024.0 * 1024.0) * 1.0) + " MB"); } catch (Exception e) { - System.err.println("Exception when dealing with " + i + jalview.bin.Console.errPrintln("Exception when dealing with " + i + "'th argument: " + args[i] + "\n" + e); } } else { - System.err.println("Ignoring argument '" + args[i] + "' (" + i + jalview.bin.Console.errPrintln("Ignoring argument '" + args[i] + "' (" + i + "'th)- not a readable file."); } i++; @@ -536,7 +559,7 @@ public class AppletFormatAdapter DataSourceType protocol = null; if (debug) { - System.out.println("resolving datasource started with:\n>>file\n" + jalview.bin.Console.outPrintln("resolving datasource started with:\n>>file\n" + file + ">>endfile"); } @@ -554,7 +577,7 @@ public class AppletFormatAdapter } if (debug) { - System.err.println("Resource '" + file + "' was " + jalview.bin.Console.errPrintln("Resource '" + file + "' was " + (rtn ? "" : "not") + " located by classloader."); } if (rtn) @@ -582,7 +605,7 @@ public class AppletFormatAdapter { if (debug) { - System.out.println( + jalview.bin.Console.outPrintln( "Trying to get contents of resource as " + protocol + ":"); } fp = new FileParse(file, protocol); @@ -594,14 +617,14 @@ public class AppletFormatAdapter { if (debug) { - System.out.println("Successful."); + jalview.bin.Console.outPrintln("Successful."); } } } catch (Exception e) { if (debug) { - System.err.println("Exception when accessing content: " + e); + jalview.bin.Console.errPrintln("Exception when accessing content: " + e); } fp = null; } @@ -609,7 +632,7 @@ public class AppletFormatAdapter { if (debug) { - System.out.println("Accessing as paste."); + jalview.bin.Console.outPrintln("Accessing as paste."); } protocol = DataSourceType.PASTE; fp = null; @@ -622,7 +645,7 @@ public class AppletFormatAdapter } } catch (Exception e) { - System.err.println("Failed to access content as paste!"); + jalview.bin.Console.errPrintln("Failed to access content as paste!"); e.printStackTrace(); fp = null; } @@ -644,20 +667,20 @@ public class AppletFormatAdapter { if (debug) { - System.out.println("Format not identified. Inaccessible file."); + jalview.bin.Console.outPrintln("Format not identified. Inaccessible file."); } return null; } if (debug) { - System.out.println("Format identified as " + idformat + jalview.bin.Console.outPrintln("Format identified as " + idformat + "and expected as " + format); } if (idformat.equals(format)) { if (debug) { - System.out.println("Protocol identified as " + protocol); + jalview.bin.Console.outPrintln("Protocol identified as " + protocol); } return protocol; } @@ -675,7 +698,7 @@ public class AppletFormatAdapter { if (debug) { - System.err.println("File deemed not accessible via " + protocol); + jalview.bin.Console.errPrintln("File deemed not accessible via " + protocol); e.printStackTrace(); } }