Merge branch 'patch/JAL-3750_JAL-3741_https_patch' into releases/Release_2_11_1_Branch
[jalview.git] / src / jalview / io /
drwxr-xr-x   ..
-rw-r--r-- 2972 AMSAFile.java
-rwxr-xr-x 10084 AlignFile.java
-rw-r--r-- 1451 AlignmentFileReaderI.java
-rw-r--r-- 1401 AlignmentFileWriterI.java
-rw-r--r-- 4133 AlignmentProperties.java
-rwxr-xr-x 52059 AnnotationFile.java
-rwxr-xr-x 18312 AppletFormatAdapter.java
-rwxr-xr-x 6217 BLCFile.java
-rw-r--r-- 1837 BackupFilenameFilter.java
-rw-r--r-- 5221 BackupFilenameParts.java
-rw-r--r-- 31369 BackupFiles.java
-rw-r--r-- 6255 BackupFilesPresetEntry.java
-rw-r--r-- 8716 BioJsHTMLOutput.java
-rwxr-xr-x 6661 ClustalFile.java
-rw-r--r-- 1463 DBRefFile.java
-rw-r--r-- 950 DataSourceType.java
-rw-r--r-- 25271 EmblFlatFile.java
-rwxr-xr-x 5072 FastaFile.java
-rwxr-xr-x 44269 FeaturesFile.java
-rw-r--r-- 9746 FileFormat.java
-rw-r--r-- 1039 FileFormatException.java
-rw-r--r-- 2443 FileFormatI.java
-rw-r--r-- 4993 FileFormats.java
-rwxr-xr-x 18508 FileLoader.java
-rwxr-xr-x 18701 FileParse.java
-rwxr-xr-x 8211 FormatAdapter.java
-rw-r--r-- 10647 HTMLOutput.java
-rw-r--r-- 5031 HtmlFile.java
-rw-r--r-- 12424 HtmlSvgOutput.java
-rwxr-xr-x 12391 IdentifyFile.java
-rw-r--r-- 1503 InputStreamParser.java
-rw-r--r-- 1127 IntKeyStringValueEntry.java
-rwxr-xr-x 11746 JPredFile.java
-rw-r--r-- 29509 JSONFile.java
-rwxr-xr-x 15833 JalviewFileChooser.java
-rwxr-xr-x 4802 JalviewFileFilter.java
-rwxr-xr-x 4528 JalviewFileView.java
-rwxr-xr-x 8514 JnetAnnotationMaker.java
-rwxr-xr-x 9547 MSFfile.java
-rwxr-xr-x 10359 ModellerDescription.java
-rwxr-xr-x 27525 NewickFile.java
-rw-r--r-- 2213 PDBFeatureSettings.java
-rwxr-xr-x 5064 PIRFile.java
-rwxr-xr-x 4360 PfamFile.java
-rw-r--r-- 9329 PhylipFile.java
-rwxr-xr-x 4406 PileUpfile.java
-rw-r--r-- 6765 RnamlFile.java
-rw-r--r-- 12501 ScoreMatrixFile.java
-rw-r--r-- 16884 SequenceAnnotationReport.java
-rw-r--r-- 8803 SimpleBlastFile.java
-rw-r--r-- 40383 StockholmFile.java
-rw-r--r-- 13129 StructureFile.java
-rw-r--r-- 17415 TCoffeeScoreFile.java
-rw-r--r-- 93726 VamsasAppDatastore.java
-rwxr-xr-x 8222 WSWUBlastClient.java
drwxr-xr-x - cache
drwxr-xr-x - gff
drwxr-xr-x - packed
drwxr-xr-x - vamsas
drwxr-xr-x - vcf