X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=56e9fa10ada182f95b7bcbb45b4a0c8c39dbde43;hb=c932f0e85a8852824cdd8ce790af68682732c85c;hp=00fcb9c39c598d12dc6d285b5b9720bb080ba129;hpb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;p=jalview.git diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java index 00fcb9c..56e9fa1 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; @@ -34,11 +38,6 @@ 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 @@ -159,13 +158,16 @@ public class AppletFormatAdapter 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()) @@ -177,11 +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); + selectedFile == null ? inFile : selectedFile, sourceType, + StructureImportSettings.getTemperatureFactorType()); } else { @@ -208,7 +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 @@ -290,7 +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 @@ -417,13 +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(); } @@ -481,7 +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(); @@ -495,36 +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++; @@ -552,7 +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"); } @@ -570,7 +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) @@ -598,7 +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); @@ -610,14 +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; } @@ -625,7 +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; @@ -638,7 +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; } @@ -660,20 +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; } @@ -691,7 +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(); } }