v1.0.5 stable release

.gitignore

@@ -3,6 +3,10 @@
 .settings/
 .idea/
 
+bin/
+jar/
+*.cfg
+
 test/
 fix/
 target/

Dockerfile

@@ -3,7 +3,7 @@ FROM ubuntu:jammy
 ENV LANG=C.UTF-8 LC_ALL=C.UTF-8
 ENV PATH /opt/conda/bin:$PATH
 
-ARG VERSION=1.0.4
+ARG VERSION=1.0.5
 ARG BUILD=0
 
 # Install dependencies

pom.xml

@@ -2,7 +2,7 @@
  <modelVersion>4.0.0</modelVersion>
  <groupId>steineggerlab</groupId>
  <artifactId>ufcg</artifactId>
- <version>1.0.4</version>
+ <version>1.0.5</version>
  <packaging>jar</packaging>
 
  <dependencies>

src/pipeline/ModuleHandler.java

@@ -1,95 +1,95 @@
-package pipeline;
-
-import envs.toolkit.Prompt;
-import module.AlignModule;
-import module.ConvertModule;
-import module.ProfileModule;
-import module.ProfileProModule;
-import module.ProfileRnaModule;
-import module.PruneModule;
-import module.TrainModule;
-import module.TreeModule;
-import module.DownloadModule;
-
-import java.util.Arrays;
-import java.util.List;
-
-public class ModuleHandler {
- private final int module;
- private final String[] args;
- public final boolean help;
-
- public ModuleHandler(int module, String[] args) {
- this.module = module;
- this.args = args;
- List<String> argList = Arrays.asList(args);
- if(argList.contains("-h") || argList.contains("-help") || argList.contains("--help")) {
- Prompt.SUPPRESS = true;
- help = true;
- } else if((module == UFCGMainPipeline.MODULE_PROFILE || module == UFCGMainPipeline.MODULE_PROFILE_RNA) && (argList.contains("-hh") || argList.contains("--hh"))) {
- Prompt.SUPPRESS = true;
- help = true;
- } else {
- help = false;
- }
- if(module == UFCGMainPipeline.MODULE_DOWNLOAD && argList.contains("-c")) {
- Prompt.SUPPRESS = true;
- }
- }
-
- private void handle_no_module() {
- UFCGMainPipeline.run(args);
- }
- private void handle_profile() {
- Prompt.talk("UFCG profile v" + UFCGMainPipeline.VERSION);
- ProfileModule.run(args);
- }
- private void handle_profile_rna() {
- Prompt.talk("UFCG profile-rna v" + UFCGMainPipeline.VERSION);
- ProfileRnaModule.run(args);
- }
- private void handle_profile_pro() {
- Prompt.talk("UFCG profile-pro v" + UFCGMainPipeline.VERSION);
- ProfileProModule.run(args);
- }
- private void handle_align() {
- Prompt.talk("UFCG align v" + UFCGMainPipeline.VERSION);
- AlignModule.run(args);
- }
- private void handle_train() {
- Prompt.talk("UFCG train v" + UFCGMainPipeline.VERSION);
- TrainModule.run(args);
- }
- private void handle_convert() {
- Prompt.talk("UFCG convert v" + UFCGMainPipeline.VERSION);
- ConvertModule.run(args);
- }
- private void handle_tree() {
- Prompt.talk("UFCG tree v" + UFCGMainPipeline.VERSION);
- TreeModule.run(args);
- }
- private void handle_prune() {
- Prompt.talk("UFCG prune v" + UFCGMainPipeline.VERSION);
- PruneModule.run(args);
- }
- private void handle_download(){
- Prompt.talk("UFCG download v" + UFCGMainPipeline.VERSION);
- DownloadModule.run(args);
- }
-
- public void handle() {
- switch(module) {
- case UFCGMainPipeline.NO_MODULE: handle_no_module(); break;
- case UFCGMainPipeline.MODULE_PROFILE: handle_profile(); break;
- case UFCGMainPipeline.MODULE_PROFILE_RNA: handle_profile_rna(); break;
- case UFCGMainPipeline.MODULE_PROFILE_PRO: handle_profile_pro(); break;
- case UFCGMainPipeline.MODULE_TREE: handle_tree(); break;
- case UFCGMainPipeline.MODULE_PRUNE: handle_prune(); break;
- case UFCGMainPipeline.MODULE_ALIGN: handle_align(); break;
- case UFCGMainPipeline.MODULE_TRAIN: handle_train(); break;
- case UFCGMainPipeline.MODULE_CONVERT: handle_convert(); break;
- case UFCGMainPipeline.MODULE_DOWNLOAD: handle_download(); break;
- default: break;
- }
- }
-}
+package pipeline;
+
+import envs.toolkit.Prompt;
+import module.AlignModule;
+import module.ConvertModule;
+import module.ProfileModule;
+import module.ProfileProModule;
+import module.ProfileRnaModule;
+import module.PruneModule;
+import module.TrainModule;
+import module.TreeModule;
+import module.DownloadModule;
+
+import java.util.Arrays;
+import java.util.List;
+
+public class ModuleHandler {
+ private final int module;
+ private final String[] args;
+ public final boolean help;
+
+ public ModuleHandler(int module, String[] args) {
+ this.module = module;
+ this.args = args;
+ List<String> argList = Arrays.asList(args);
+ if(argList.contains("-h") || argList.contains("-help") || argList.contains("--help")) {
+ Prompt.SUPPRESS = true;
+ help = true;
+ } else if((module == UFCGMainPipeline.MODULE_PROFILE || module == UFCGMainPipeline.MODULE_PROFILE_RNA) && (argList.contains("-hh") || argList.contains("--hh"))) {
+ Prompt.SUPPRESS = true;
+ help = true;
+ } else {
+ help = false;
+ }
+ if(module == UFCGMainPipeline.MODULE_DOWNLOAD && argList.contains("-c")) {
+ Prompt.SUPPRESS = true;
+ }
+ }
+
+ private void handle_no_module() {
+ UFCGMainPipeline.run(args);
+ }
+ private void handle_profile() {
+ Prompt.talk("UFCG profile v" + UFCGMainPipeline.VERSION);
+ ProfileModule.run(args);
+ }
+ private void handle_profile_rna() {
+ Prompt.talk("UFCG profile-rna v" + UFCGMainPipeline.VERSION);
+ ProfileRnaModule.run(args);
+ }
+ private void handle_profile_pro() {
+ Prompt.talk("UFCG profile-pro v" + UFCGMainPipeline.VERSION);
+ ProfileProModule.run(args);
+ }
+ private void handle_align() {
+ Prompt.talk("UFCG align v" + UFCGMainPipeline.VERSION);
+ AlignModule.run(args);
+ }
+ private void handle_train() {
+ Prompt.talk("UFCG train v" + UFCGMainPipeline.VERSION);
+ TrainModule.run(args);
+ }
+ private void handle_convert() {
+ Prompt.talk("UFCG convert v" + UFCGMainPipeline.VERSION);
+ ConvertModule.run(args);
+ }
+ private void handle_tree() {
+ Prompt.talk("UFCG tree v" + UFCGMainPipeline.VERSION);
+ TreeModule.run(args);
+ }
+ private void handle_prune() {
+ Prompt.talk("UFCG prune v" + UFCGMainPipeline.VERSION);
+ PruneModule.run(args);
+ }
+ private void handle_download(){
+ Prompt.talk("UFCG download v" + UFCGMainPipeline.VERSION);
+ DownloadModule.run(args);
+ }
+
+ public void handle() {
+ switch(module) {
+ case UFCGMainPipeline.NO_MODULE: handle_no_module(); break;
+ case UFCGMainPipeline.MODULE_PROFILE: handle_profile(); break;
+ case UFCGMainPipeline.MODULE_PROFILE_RNA: handle_profile_rna(); break;
+ case UFCGMainPipeline.MODULE_PROFILE_PRO: handle_profile_pro(); break;
+ case UFCGMainPipeline.MODULE_TREE: handle_tree(); break;
+ case UFCGMainPipeline.MODULE_PRUNE: handle_prune(); break;
+ case UFCGMainPipeline.MODULE_ALIGN: handle_align(); break;
+ case UFCGMainPipeline.MODULE_TRAIN: handle_train(); break;
+ case UFCGMainPipeline.MODULE_CONVERT: handle_convert(); break;
+ case UFCGMainPipeline.MODULE_DOWNLOAD: handle_download(); break;
+ default: break;
+ }
+ }
+}

src/pipeline/UFCGMainPipeline.java

@@ -36,9 +36,9 @@
 
 @SuppressWarnings("restriction")
 public class UFCGMainPipeline {
- public static final String VERSION = "1.0.4";
- public static final Boolean STABLE = false;
- public static final String RELEASE_DATE = "May 2023";
+ public static final String VERSION = "1.0.5";
+ public static final Boolean STABLE = true;
+ public static final String RELEASE_DATE = "Aug 2023";
  public static final String CITATION = " Kim, D., Gilchrist, C.L.M., Chun, J. & Steinegger, M. (2023)\n"
  + " UFCG: database of universal fungal core genes and pipeline for genome-wide phylogenetic analysis of fungi.\n"
  + " Nucleic Acids Research, 51(D1), D777-D784, doi:10.1093/nar/gkac894.\n";

src/tree/tools/Arguments.java

@@ -1,47 +1,47 @@
-package tree.tools;
-
-import java.util.Hashtable;
-
-@Deprecated
-public class Arguments {
- public Hashtable<String,String> hash = new Hashtable<>();
- public String[] args;
-
- int process_next(int index)
- {
- if (index==args.length-1) {
- hash.put(args[index], "");// for last, just add
- return args.length;
- }
- if (args[index+1].startsWith("-")) {
-
- hash.put(args[index], "");
- return index;
- }
- hash.put(args[index],args[index+1]);
- return index+1;
- }
-
- public Arguments(String[] args){
- this.args = args;
- for (int i=0; i<args.length; i++)
- {
- if (args[i].startsWith("-"))
- {
- i=process_next(i);
- }
- }
- }
-
- /**
- * 
- * @param arg - tag of argument
- * @return return null if no exist matched tag, or 
- * empty string if anything value is not assigned for the tag 
- */
- public String get(String arg)
- {
- return hash.get(arg);
- }
-
+package tree.tools;
+
+import java.util.Hashtable;
+
+@Deprecated
+public class Arguments {
+ public Hashtable<String,String> hash = new Hashtable<>();
+ public String[] args;
+
+ int process_next(int index)
+ {
+ if (index==args.length-1) {
+ hash.put(args[index], "");// for last, just add
+ return args.length;
+ }
+ if (args[index+1].startsWith("-")) {
+
+ hash.put(args[index], "");
+ return index;
+ }
+ hash.put(args[index],args[index+1]);
+ return index+1;
+ }
+
+ public Arguments(String[] args){
+ this.args = args;
+ for (int i=0; i<args.length; i++)
+ {
+ if (args[i].startsWith("-"))
+ {
+ i=process_next(i);
+ }
+ }
+ }
+
+ /**
+ * 
+ * @param arg - tag of argument
+ * @return return null if no exist matched tag, or 
+ * empty string if anything value is not assigned for the tag 
+ */
+ public String get(String arg)
+ {
+ return hash.get(arg);
+ }
+
 }