<FONT color="green">534</FONT>                            + (exclude_classes.size() == 0 ? "basic" : String<a name="line.534"></a>
<FONT color="green">535</FONT>                                    .valueOf(exclude_classes.size()))<a name="line.535"></a>
<FONT color="green">536</FONT>                            + " type(s) and "<a name="line.536"></a>
<FONT color="green">537</FONT>                            + (exclude_archives.size() == 0 ? "no" : String<a name="line.537"></a>
<FONT color="green">538</FONT>                                    .valueOf(exclude_archives.size()))<a name="line.538"></a>
<FONT color="green">539</FONT>                            + " archive(s) to exclude started.");<a name="line.539"></a>
<FONT color="green">540</FONT>                    start = System.currentTimeMillis();<a name="line.540"></a>
<FONT color="green">541</FONT>                    String[] classes = new String[exclude_classes.size()];<a name="line.541"></a>
<FONT color="green">542</FONT>                    for (int i = 0; i &lt; exclude_classes.size(); ++i)<a name="line.542"></a>
<FONT color="green">543</FONT>                        classes[i] = (String) exclude_classes.get(i);<a name="line.543"></a>
<FONT color="green">544</FONT>                    String[] archives = new String[exclude_archives.size()];<a name="line.544"></a>
<FONT color="green">545</FONT>                    for (int i = 0; i &lt; exclude_archives.size(); ++i)<a name="line.545"></a>
<FONT color="green">546</FONT>                        archives[i] = (String) exclude_archives.get(i);<a name="line.546"></a>
<FONT color="green">547</FONT>                    Analyzer analyzer = new Analyzer(classes, archives, new String[0], quiet,<a name="line.547"></a>
<FONT color="green">548</FONT>                            verbose);<a name="line.548"></a>
<FONT color="green">549</FONT>                    excludes = analyzer.analyze();<a name="line.549"></a>
<FONT color="green">550</FONT>                    end = System.currentTimeMillis();<a name="line.550"></a>
<FONT color="green">551</FONT>                    System.err.print("Analysis ended after "<a name="line.551"></a>
<FONT color="green">552</FONT>                            + String.valueOf((end - start) / 1000.0) + " s. ");<a name="line.552"></a>
<FONT color="green">553</FONT>                    System.err.println(String.valueOf(excludes.length)<a name="line.553"></a>
<FONT color="green">554</FONT>                            + " type(s) will be excluded.");<a name="line.554"></a>
<FONT color="green">555</FONT>                } else<a name="line.555"></a>
<FONT color="green">556</FONT>                    excludes = null;<a name="line.556"></a>
<FONT color="green">557</FONT>                // analyze the compounds to include in the processing<a name="line.557"></a>
<FONT color="green">558</FONT>                System.err.println("Analysis of "<a name="line.558"></a>
<FONT color="green">559</FONT>                        + (include_classes.size() == 0 ? "basic" : String<a name="line.559"></a>
<FONT color="green">560</FONT>                                .valueOf(include_classes.size()))<a name="line.560"></a>
<FONT color="green">561</FONT>                        + " type(s) and "<a name="line.561"></a>
<FONT color="green">562</FONT>                        + (include_archives.size() == 0 ? "no" : String<a name="line.562"></a>
<FONT color="green">563</FONT>                                .valueOf(include_archives.size()))<a name="line.563"></a>
<FONT color="green">564</FONT>                        + " archive(s) filtered by "<a name="line.564"></a>
<FONT color="green">565</FONT>                        + (include_scopes.size() == 0 ? "no" : String.valueOf(include_scopes<a name="line.565"></a>
<FONT color="green">566</FONT>                                .size())) + " package(s) to include started.");<a name="line.566"></a>
<FONT color="green">567</FONT>                start = System.currentTimeMillis();<a name="line.567"></a>
<FONT color="green">568</FONT>                String[] classes = new String[include_classes.size()];<a name="line.568"></a>
<FONT color="green">569</FONT>                for (int i = 0; i &lt; include_classes.size(); ++i)<a name="line.569"></a>
<FONT color="green">570</FONT>                    classes[i] = (String) include_classes.get(i);<a name="line.570"></a>
<FONT color="green">571</FONT>                String[] archives = new String[include_archives.size()];<a name="line.571"></a>
<FONT color="green">572</FONT>                for (int i = 0; i &lt; include_archives.size(); ++i)<a name="line.572"></a>
<FONT color="green">573</FONT>                    archives[i] = (String) include_archives.get(i);<a name="line.573"></a>
<FONT color="green">574</FONT>                String[] scopes = new String[include_scopes.size()];<a name="line.574"></a>
<FONT color="green">575</FONT>                for (int i = 0; i &lt; include_scopes.size(); ++i)<a name="line.575"></a>
<FONT color="green">576</FONT>                    scopes[i] = ((String) include_scopes.get(i));<a name="line.576"></a>
<FONT color="green">577</FONT>                Analyzer analyzer = incomplete ? new Analyzer(classes, archives, scopes,<a name="line.577"></a>
<FONT color="green">578</FONT>                        excludes, quiet, verbose) : new Analyzer(classes, archives, scopes,<a name="line.578"></a>
<FONT color="green">579</FONT>                        quiet, verbose);<a name="line.579"></a>
<FONT color="green">580</FONT>                CompoundInfo[] includes = analyzer.analyze();<a name="line.580"></a>
<FONT color="green">581</FONT>                end = System.currentTimeMillis();<a name="line.581"></a>
<FONT color="green">582</FONT>                System.err.print("Analysis ended after "<a name="line.582"></a>
<FONT color="green">583</FONT>                        + String.valueOf((end - start) / 1000.0) + " s. ");<a name="line.583"></a>
<FONT color="green">584</FONT>                System.err.println(String.valueOf(includes.length)<a name="line.584"></a>
<FONT color="green">585</FONT>                        + " type(s) will be extracted.");<a name="line.585"></a>
<FONT color="green">586</FONT>                // extract the selected compounds<a name="line.586"></a>
<FONT color="green">587</FONT>                System.err.println("Extraction started.");<a name="line.587"></a>
<FONT color="green">588</FONT>                start = System.currentTimeMillis();<a name="line.588"></a>
<FONT color="green">589</FONT>                Extractor extractor = new Extractor(quiet, verbose);<a name="line.589"></a>
<FONT color="green">590</FONT>                extractor.outputHeader();<a name="line.590"></a>
<FONT color="green">591</FONT>                extractor.extract(includes);<a name="line.591"></a>
<FONT color="green">592</FONT>                end = System.currentTimeMillis();<a name="line.592"></a>
<FONT color="green">593</FONT>                System.err.println("Extraction ended after "<a name="line.593"></a>
<FONT color="green">594</FONT>                        + String.valueOf((end - start) / 1000.0) + " s.");<a name="line.594"></a>
<FONT color="green">595</FONT>            } catch (Exception e) {<a name="line.595"></a>
<FONT color="green">596</FONT>                System.err.println(e.toString());<a name="line.596"></a>
<FONT color="green">597</FONT>                System.exit(1);<a name="line.597"></a>
<FONT color="green">598</FONT>            }<a name="line.598"></a>
<FONT color="green">599</FONT>        }<a name="line.599"></a>
<FONT color="green">600</FONT>    <a name="line.600"></a>
<FONT color="green">601</FONT>    }<a name="line.601"></a>




























































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