X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=8b7a4c2389ea3a30d47945dcefed3e6fc52fad45;hb=e57f77dc13f5a295cf49a403da05770a68a6e22b;hp=c25d3d9cdd0b58236a5b6aa8b9faa407e4d98513;hpb=8286731258d314669ee6facb627947fe159ac1eb;p=jalview.git diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java index c25d3d9..8b7a4c2 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.IOException; +import java.io.InputStream; +import java.util.List; import java.util.Locale; import jalview.api.AlignExportSettingsI; @@ -28,18 +32,12 @@ 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; -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 @@ -155,17 +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()) @@ -177,10 +179,16 @@ 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 { @@ -193,9 +201,12 @@ public class AppletFormatAdapter ((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)); @@ -204,8 +215,8 @@ public class AppletFormatAdapter } catch (Exception e) { e.printStackTrace(); - System.err.println("Failed to read alignment using the '" + fileFormat - + "' reader.\n" + e); + jalview.bin.Console.errPrintln("Failed to read alignment using the '" + + fileFormat + "' reader.\n" + e); if (e.getMessage() != null && e.getMessage().startsWith(INVALID_CHARACTERS)) @@ -286,8 +297,8 @@ public class AppletFormatAdapter } catch (Exception e) { e.printStackTrace(); - System.err.println("Failed to read alignment using the '" + format - + "' reader.\n" + e); + jalview.bin.Console.errPrintln("Failed to read alignment using the '" + + format + "' reader.\n" + e); if (e.getMessage() != null && e.getMessage().startsWith(INVALID_CHARACTERS)) @@ -413,13 +424,13 @@ public class AppletFormatAdapter String afileresp = afile.print(seqs, jvsuffix); if (afile.hasWarningMessage()) { - System.err.println("Warning raised when writing as " + format - + " : " + afile.getWarningMessage()); + 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(); } @@ -427,23 +438,23 @@ 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(Locale.ROOT).trim(); @@ -477,7 +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(); @@ -491,37 +502,39 @@ public class AppletFormatAdapter memf += r.totalMemory() - r.freeMemory(); if (al != null) { - System.out.println("Alignment contains " + al.getHeight() - + " sequences and " + al.getWidth() + " columns."); + 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 - + "'th)- not a readable file."); + jalview.bin.Console.errPrintln("Ignoring argument '" + args[i] + + "' (" + i + "'th)- not a readable file."); } i++; } @@ -548,8 +561,9 @@ public class AppletFormatAdapter DataSourceType protocol = null; if (debug) { - System.out.println("resolving datasource started with:\n>>file\n" - + file + ">>endfile"); + jalview.bin.Console + .outPrintln("resolving datasource started with:\n>>file\n" + + file + ">>endfile"); } // This might throw a security exception in certain browsers @@ -566,7 +580,7 @@ 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) @@ -594,7 +608,7 @@ 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); @@ -606,14 +620,15 @@ 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; } @@ -621,7 +636,7 @@ public class AppletFormatAdapter { if (debug) { - System.out.println("Accessing as paste."); + jalview.bin.Console.outPrintln("Accessing as paste."); } protocol = DataSourceType.PASTE; fp = null; @@ -634,7 +649,8 @@ 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; } @@ -656,20 +672,22 @@ 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; } @@ -687,7 +705,8 @@ 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(); } }