DocumentOperation 在部署时表现不同

你好

不知何故，我在这里看到了一个模式。我有一个 DocumentOperation，它在从 IDE 启动时工作正常，但在作为插件运行时表现不同。 

这可能与： https://support.geneious.com/hc/en-us/community/posts/115001972371-Plugin-works-only-from-IDE-not-in-packaged-form-Why有关 

包 de.mpicbg.gef;

导入 com.biomatters.geneious.publicapi.components.Dialogs;
导入 com.biomatters.geneious.publicapi.databaseservice.DatabaseServiceException;
导入 com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument;
导入 com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation;
导入 com.biomatters.geneious.publicapi.documents.sequence.SequenceDocument;
导入 com.biomatters.geneious.publicapi.plugin.*;
导入 jebl.util.ProgressListener;

导入 java.util.ArrayList;
导入 java.util.LinkedList;
导入 java.util.List;

 /**
 * 由 Stephan Janosch 于 17 年 11 月 17 日创建。
*/
公共类 GefPrimerOperation 扩展了 DocumentOperation { 


 @覆盖
公共 GeneiousActionOptions getActionOptions() {
 GeneiousActionOptions actionOptions = new GeneiousActionOptions("围绕注释创建引物", "围绕注释生成引物", null, GeneiousActionOptions.Category.None);
 actionOptions.setMainMenuLocation(GeneiousActionOptions.MainMenu.Sequence);
 actionOptions.setInMainToolbar(false);

返回操作选项；
 }

 @覆盖
公共字符串 getHelp() {
返回 ””;
 }

 @覆盖
公共 DocumentSelectionSignature[] getSelectionSignatures() {
 DocumentSelectionSignature sequenceSelSig = new DocumentSelectionSignature(SequenceDocument.class, 1, 100);
返回新的 DocumentSelectionSignature[]{sequenceSelSig};
 } 


 @覆盖
public void performOperation(AnnotatedPluginDocument[] annotatedDocuments, ProgressListener progressListener, Options options, SequenceSelection sequenceSelection, OperationCallback callback) 抛出 DocumentOperationException {

 String tagType = options.getValueAsString("tagType");

 int i = 0;
 for (AnnotatedPluginDocument 文档：annotatedDocuments) {
我++;
 progressListener.setProgress(i, annotatedDocuments.length);
 SequenceDocument sequenceDocument = (SequenceDocument) document.getDocument();
 //找到标签
SequenceAnnotation tagAnnotation = null;
 for (SequenceAnnotation 注解：sequenceDocument.getSequenceAnnotations()) {
 if (tagAnnotation == null && annotation.getType().equalsIgnoreCase(tagType))
 tagAnnotation = 注释；
 else if (annotation.getType().equalsIgnoreCase(tagType))
 throw new DocumentOperationException("在以下位置找到更多的标签：" + document.getName());
 }

 if (tagAnnotation == null)
 throw new DocumentOperationException("在以下位置找不到标签：" + document.getName());

 String fromPosition = String.valueOf(tagAnnotation.getInterval().getMinimumIndex());
 String toPosition = String.valueOf(tagAnnotation.getInterval().getMaximumIndex());

 DocumentOperation primeOperation = PluginUtilities.getDocumentOperation("Operation_com.biomatters.plugins.primerDesign.DesignAnnotationGenerator");

选项primerOperationOptions =primerOperation.getOptions(document);

 // System.out.println(primerOperationOptions.getDescriptionAndState());
 // System.out.println("可用选项：" +primerOperationOptions.getNamesAndValues(true));

断言primerOperationOptions.setStringValue("taskOptions.chooser", "designNewOptions");
断言primerOperationOptions.setStringValue("taskOptions.designNewOptions.oligosToPickOptions.forwardOption", "true");
断言primerOperationOptions.setStringValue("taskOptions.designNewOptions.oligosToPickOptions.reverseOption", "true");
断言primerOperationOptions.setStringValue("taskOptions.designNewOptions.oligosToPickOptions.probeOption", "false");

断言primerOperationOptions.setStringValue("panelForRegionType.designRegionTypeOption", "genericOptionValue");
断言primerOperationOptions.setStringValue("panelForRegionType.genericRegionOptions.enableIncludedRegionOption", "false");

断言primerOperationOptions.setStringValue("panelForRegionType.genericRegionOptions.enableTargetRegionOption", "true");
断言primerOperationOptions.setStringValue("panelForRegionType.genericRegionOptions.targetRegionFromOption", fromPosition);
断言primerOperationOptions.setStringValue("panelForRegionType.genericRegionOptions.targetRegionToOption", toPosition);

断言primerOperationOptions.setStringValue("panelForRegionType.genericRegionOptions.enableProductSizeOption", "true");
断言primerOperationOptions.setStringValue("panelForRegionType.genericRegionOptions.productSizeFromOption", options.getValueAsString("productSizeFromOption"));
断言primerOperationOptions.setStringValue("panelForRegionType.genericRegionOptions.productSizeToOption", options.getValueAsString("productSizeToOption"));

断言primerOperationOptions.setStringValue("panelForRegionType.genericRegionOptions.enableOptimalProductSizeOption", "false");
断言primerOperationOptions.setStringValue("panelForRegionType.genericRegionOptions.numPairsOption", "1"); 


尝试 {
 callback.setSubFolder("启动序列");
 } catch (DatabaseServiceException e) {
 e.printStackTrace();
 }
 primerOperation.performOperation(new AnnotatedPluginDocument[]{document},ProgressListener.EMPTY,primerOperationOptions,sequenceSelection,callback);

 }

 } 


 @覆盖
公共选项 getOptions(DocumentOperationInput operationInput) 抛出 DocumentOperationException {
选项 options = new Options(getClass());
 options.addLabel("选择标签的注释类型：");
 Options.OptionValue preselectedTag = null;
列表<String>tagTypeList = 新的 LinkedList<String> ();
 for (AnnotatedPluginDocument doc : operationInput.getInputDocumentsList()) {
 SequenceDocument 序列文档 = null;
 if (doc.getDocument() instanceof SequenceDocument) {
 sequenceDocument = (SequenceDocument) doc.getDocument();
 }
 if (sequenceDocument == null)
继续;
 for (SequenceAnnotation 注解：sequenceDocument.getSequenceAnnotations()) {
 String annoType = annotation.getType().toLowerCase();
 if (!tagTypeList.contains(annoType) && annoType != null && !annoType.isEmpty())
 tagTypeList.add(annoType);
 }
 }

如果 (tagTypeList.isEmpty())
 throw new DocumentOperationException("没有找到注释");

 final Options.OptionValue[] optionValues = new Options.OptionValue[tagTypeList.size()];
 int i = 0;
 for (String tagTypeString : tagTypeList) {
 Options.OptionValue value = new Options.OptionValue(tagTypeString, tagTypeString);
选项值[i] = 值；
 if (tagTypeString.equalsIgnoreCase("tag"))
 preselectedTag = optionValues[i];
我++;
 }
 options.addComboBoxOption("tagType", "选择标记的注释类型", optionValues, preselectedTag);
 options.addIntegerOption("productSizeFromOption", "product size from", 1000);
 options.addIntegerOption("productSizeToOption", "产品尺寸到", 3000);

退货选项；
 }
 }

我检查了我的项目设置，它们符合设置指南。

为了完整起见，我也发布了我的构建文件：

<?xml version="1.0" ?>

<project name="GefPrimerPlugin" default="distribute" basedir=".">

<property file="plugin.properties"/>
<property name="build" location="build"/>
<property name="classes" location="classes"/>
<property name="src" location="src"/>

<path id="classpath">
<fileset dir="../../geneiousPlugins/geneious-10.2.3-devkit/examples/GeneiousFiles/lib">
<include name="GeneiousPublicAPI.jar"/>
<include name="jdom.jar"/>
<include name="jebl.jar"/>
</fileset>
</path>

<target name= "distribute" depends="build">
<copy file="${build}/${short-plugin-name}.jar" tofile="${build}/${short-plugin-name}.gplugin"/>
<echo message="Created ${build}/${short-plugin-name}.gplugin"/>

<!--If your plugin consists of a folder you should build it into
一个扩展名为 gplugin 的 zip 文件。请参阅下面的评论示例。
删除上面的行并取消注释这些以使用--> 
<!--
 <zip zipfile="${build}/${short-plugin-name}.gplugin">
 <fileset dir="${build}/${plugin-name}"/>
 </zip>
 -->
</target>

<target name="build" depends="compile">
<jar jarfile="${build}/${short-plugin-name}.jar">
<fileset dir="${classes}"/>
<fileset dir="">
<include name="plugin.properties"/>
</fileset>
</jar>

<!--build example for folder type plugin.删除上面
行并取消注释这些以使用--> 
<!--
 <jar jarfile="${build}/${short-plugin-name}.jar">
 <fileset dir="${classes}"/>
 </jar>
 <mkdir dir="${build}/${plugin-name}"/>
 <copy todir="${build}/${plugin-name}">
 <fileset dir="${build}">
 <include name="ExtraFiles"/>
 <include name="ExtraFiles/*"/>
 <include name="${short-plugin-name}.jar"/>
 </fileset>
 <fileset dir="docs">
 <include name="readme.txt"/>
 </fileset>
 </copy>
 -->
</target>

<target name="compile" depends="prepare">
<javac target="1.8" source="1.8" destdir="${classes}" debug="true">
<classpath refid="classpath"/>
<src path="${src}"/>
</javac>
</target>

<target name="prepare">
<mkdir dir="${build}"/>
<mkdir dir="${classes}"/>
</target>

<target name="clean">
<delete dir="${build}"/>
<delete dir="${classes}"/>
</target>
</project>

一头雾水，
斯蒂芬