From 85307c78748080deedadf616a37a03f2f10a3a7d Mon Sep 17 00:00:00 2001 From: owlang Date: Thu, 7 Jan 2021 11:12:09 -0500 Subject: [PATCH] hotfix v0.13 bug in CoordMan tool gui output file Output path directory, not file, given in three Coordinate Manipulation tools in the GUI window_interface classes. CLI versions unaffected. The recent release included a shift for the script classes to take the output filename path instead of the output directory name path. The new output filename was created within the window classes but the directory name was passed instead for three of the Coordinate Manipulation group window_interface classes. This commit both fixes this bug and renames the JAR file, window title, and tool version for a new v0.13 release. --- build.gradle | 2 +- src/main/ScriptManager.java | 2 +- src/main/ScriptManagerGUI.java | 2 +- .../BED_Manipulation/BEDtoGFFWindow.java | 4 ++-- .../GFF_Manipulation/ExpandGFFWindow.java | 6 +++--- .../GFF_Manipulation/GFFtoBEDWindow.java | 4 ++-- 6 files changed, 10 insertions(+), 10 deletions(-) diff --git a/build.gradle b/build.gradle index 15f8793f9..87780eb74 100644 --- a/build.gradle +++ b/build.gradle @@ -9,7 +9,7 @@ apply plugin: 'eclipse' sourceSets.main.java.srcDirs = ['src'] mainClassName = "main.ScriptManager" -version = 'v0.13-dev' +version = 'v0.13' sourceCompatibility = 1.8 targetCompatibility = 1.8 diff --git a/src/main/ScriptManager.java b/src/main/ScriptManager.java index 96485cb71..1937af6a4 100755 --- a/src/main/ScriptManager.java +++ b/src/main/ScriptManager.java @@ -70,7 +70,7 @@ Read_AnalysisCLI.class, Sequence_AnalysisCLI.class }, - version = "ScriptManager-v0.13-dev", + version = "ScriptManager-v0.13", mixinStandardHelpOptions = true, description = "Choose a tool directory from below to see more command-line tool options.", exitCodeOnInvalidInput = 1, diff --git a/src/main/ScriptManagerGUI.java b/src/main/ScriptManagerGUI.java index ef73b4cfa..421604740 100755 --- a/src/main/ScriptManagerGUI.java +++ b/src/main/ScriptManagerGUI.java @@ -55,7 +55,7 @@ import window_interface.Figure_Generation.MergeHeatMapWindow; public class ScriptManagerGUI { - public static final String VERSION = "0.13-dev"; + public static final String VERSION = "0.13"; private JFrame frmScriptManager; /** diff --git a/src/window_interface/Coordinate_Manipulation/BED_Manipulation/BEDtoGFFWindow.java b/src/window_interface/Coordinate_Manipulation/BED_Manipulation/BEDtoGFFWindow.java index c2b3a87c8..49b1815ce 100644 --- a/src/window_interface/Coordinate_Manipulation/BED_Manipulation/BEDtoGFFWindow.java +++ b/src/window_interface/Coordinate_Manipulation/BED_Manipulation/BEDtoGFFWindow.java @@ -62,7 +62,7 @@ public Void doInBackground() throws IOException { if(OUTPUT_PATH == null) OUT_FILE = new File( gffName ); else OUT_FILE = new File( OUTPUT_PATH + File.separator + gffName ); // Execute conversion and update progress - BEDtoGFF.convertBEDtoGFF(OUTPUT_PATH, XBED); + BEDtoGFF.convertBEDtoGFF(OUT_FILE, XBED); int percentComplete = (int)(((double)(x + 1) / BEDFiles.size()) * 100); setProgress(percentComplete); } @@ -197,4 +197,4 @@ public void massXable(Container con, boolean status) { if(c instanceof Container) { massXable((Container)c, status); } } } -} \ No newline at end of file +} diff --git a/src/window_interface/Coordinate_Manipulation/GFF_Manipulation/ExpandGFFWindow.java b/src/window_interface/Coordinate_Manipulation/GFF_Manipulation/ExpandGFFWindow.java index cf0775563..d0bfe73e1 100644 --- a/src/window_interface/Coordinate_Manipulation/GFF_Manipulation/ExpandGFFWindow.java +++ b/src/window_interface/Coordinate_Manipulation/GFF_Manipulation/ExpandGFFWindow.java @@ -76,8 +76,8 @@ public Void doInBackground() throws IOException { File OUT_FILE = null; if(OUTPUT_PATH == null) OUT_FILE = new File( newName ); else OUT_FILE = new File( OUTPUT_PATH + File.separator + newName ); - // Execute expansion and update progress - ExpandGFF.expandGFFBorders(OUTPUT_PATH, XGFF, SIZE, rdbtnExpandFromCenter.isSelected()); + // Execute expansion and update progress + ExpandGFF.expandGFFBorders(OUT_FILE, XGFF, SIZE, rdbtnExpandFromCenter.isSelected()); int percentComplete = (int)(((double)(x + 1) / GFFFiles.size()) * 100); setProgress(percentComplete); } @@ -245,4 +245,4 @@ public void massXable(Container con, boolean status) { if(c instanceof Container) { massXable((Container)c, status); } } } -} \ No newline at end of file +} diff --git a/src/window_interface/Coordinate_Manipulation/GFF_Manipulation/GFFtoBEDWindow.java b/src/window_interface/Coordinate_Manipulation/GFF_Manipulation/GFFtoBEDWindow.java index 229c74a7d..3f3364444 100644 --- a/src/window_interface/Coordinate_Manipulation/GFF_Manipulation/GFFtoBEDWindow.java +++ b/src/window_interface/Coordinate_Manipulation/GFF_Manipulation/GFFtoBEDWindow.java @@ -62,7 +62,7 @@ public Void doInBackground() throws IOException { if(OUTPUT_PATH == null) OUT_FILE = new File( bedName ); else OUT_FILE = new File( OUTPUT_PATH + File.separator + bedName ); // Execute conversion and update progress - GFFtoBED.convertGFFtoBED(OUTPUT_PATH, XGFF); + GFFtoBED.convertGFFtoBED(OUT_FILE, XGFF); int percentComplete = (int)(((double)(x + 1) / BEDFiles.size()) * 100); setProgress(percentComplete); } @@ -197,4 +197,4 @@ public void massXable(Container con, boolean status) { if(c instanceof Container) { massXable((Container)c, status); } } } -} \ No newline at end of file +}